Recommended Mods

Since there are many mods here's some of my recommendations for best mods, but change them around depending on your playstyle and weapon. For a full list of mods available please refer to the wiki at http://warframe.wikia.com/wiki/Mods

Try to level important mods together instead of trying to max only one. For instance if you have a slow firing weapon don't level up serration so much that you can't put speed trigger in. You'll be happier with some attack speed and good damage.
As this post is quite long I have split it into sections:

Rifle mods
Pistol mods
Shotgun mods
Melee mods
Elemental damage system
Enemy weakness table
Warframe mods
Aura mods
Sentinels

Update 11: A new damage system was introduced along with new mods. Each weapon now also gives three different types of damage: impact, puncture and slash. Each can be increased by use of their respective mod cards.

Damage = impact + puncture + slash + elemental

After spending time testing the new system it appears that the best general damage is still from cards that increase all damage such as serration (others that are listed below in their respective categories) and an elemental mod.

However if a weapon has a lot more of one type of damage than the others such as a flux rifle, which has 120 slash and 15 for impact and puncture, then using the new mod card that increases slash damage (Sawtooth clip in this case) will be effective. The new cards are best for melee since you can level them up to give 90% extra. Each type is good against different enemies.

Corpus humans – Impact, slash
Corpus robots – Impact
Grineer – Puncture, slash
Infested – Slash

The new damage mods can be upgraded to give a maximum of 30% for rifles and shotguns, 60% for pistols and 90% for melee weapons.
A new element system was also introduced but more on that below.

Weapon Mods

Rifle mods:

Serration – Gives more damage. Very difficult to max but try at least 75% (takes up capacity of 8). Once your weapon has an orokin try to make this at least 150%.

Sawtooth clip – Increases the slash damage of rifles

Rupture – Increases the impact damage of rifles

Piercing hit – Increases armor piercing damage. Good for all enemies and should be at least 40% (takes up capacity of 7). For enemies that don't have armor its still useful as it counts as elemental damage. As of Update 11 this mod is useless!! As it now only increases puncture damage by maximum of 30%. So it's good for guns with high puncture like the boltor. Before update 11 you could upgrade this to give 90% armour piercing :-(

Split chamber – Each bullet has a chance of shooting one more without costing ammo (multishot). Although a very good mod and important for dps this mod is VERY hard to find. It also costs a minimum of 10 to equip, so not recommended till you potato your weapon.

Speed Trigger – Increases fire rate. I find 30% (takes up 6 mod capacity) enough for most guns as any higher would mean too much ammo loss.

Bane of Corpus/Infested/Grineer - Increases base damage and any elemental mod damage. Most missions have one main type so exchange mods as needed.

Infected Clip – Poison damage which is good against grineer but weak against infested and robots. However it bypasses shields.

Cyro rounds – Ice damage. Very good for enemies that have shields and also slows down enemies.

Stormbringer – Electric damage that's effective against corpus as it stuns them if they have no shield

Hellfire – Fire damage which is best against infested

Fast hands – Increases reload speed. Use this if your gun takes ages to reload.

Wildfire – fire damage and magazine capacity. A nightmare mod that you get randomly for finishing a nightmare mission. It can be very hard to get so I wouldn't waste time getting it if you're starting out.

Shred – fire rate and punch through (bullet goes through enemies and objects). Another nightmare mod that I would not waste time getting till later.

Metal Auger – As of update 11 this can be maxed to give 2.1 metres punch through. This can be quite useful when fighting enemies that are bunched together or those grineer who have shields as this mod allows you to shoot through them.

Pistol mods:

Pistol mods get the best stat increases per rank up.

Hornet strike – Increases damage. At least 100% that takes up a capacity of 8

No return/Razor shot/Concussion rounds – Increases puncture/slash/impact damage respectively

Gunslinger – increase firerate

Expel infested/Grineer/Corpus - Increases damage, exchange as needed.

Barrel diffusion – Multishot. Yes its hard to find.

Pathogen Rounds  – Adds poison damage to pistols

Deep freeze – Ice damage

Heated charge – Fire damage

Convulsion – Electric damage

Quickdraw – Faster reload speed

Seeker – Allows your weapon to punch through. Beware this mod will use up 11 slot capacity to equip.

Lethal torrent – a nightmare mod that gives multishot chance and fire rate. It stacks with barrel diffusion so if you max both you get an 180% chance of multishot. That means you're guaranteed 2 shots from 1 bullet and an 80% chance of a 3^rd shot! Definitely try and get this when you're ranked up well.

Shotgun mods:

Point Blank – Increases damage

Flechette/Disruptor/Shredder – Increases puncture/impact/slash damage

Tactical pump – faster reload speed

Cleanse infested/Grineer/Corpus – Increases damage, exchange as needed.

Hell's Chamber – Multishot

Contagious Spread  – Adds poison damage to shotguns

Chilling Grasp – Ice damage

Incendiary coat – Fire damage

Charged Shell – Electric damage

Blaze – Nightmare mod that gives Damage and Fire damage

Accelerated blast – Nightmare mod that gives armour penetration and firerate.

Seeking force – Allows bullets to punch through

Melee:

As of update 13, melee 2 has arrived removing charge attacks and introducing a new combo system. 
You can either press e to do normal melee whilst holding your primary/secondary weapon or equip melee weapon by holding down the f key. In melee mode holding the right mouse button will block in the direction you are facing (takes up stamina). Holding the left button will add 20% extra damage when you press e but this will take up energy. 
In order to use the combo system you will have to find and equip stance cards. Each type of melee will have their own stance card and you can find out the combos when equipping them. Also equipping a stance card works like an aura card in that it increases the mod capacity for your melee weapon.

There are two ways of playing with a melee weapon and its important mod wise that you find out which style you prefer.

You can either spam the melee button using weapons that have fast attack speed or use charged attacks by holding down the melee button.

For charged attacks:

Killing blow – Increases charged attack damage

Reflex coil – Lets you charge attacks faster

Rending Strike – Nightmare mod that adds puncture damage and increases charged damage

Focus energy – Nightmare mod that increases charge speed and adds electric damage

Fury – Speeds up motion of charged attack and also increases attack speed

For normal attacks:

Pressure point – Increases base damage but does not help charged attacks

Fury – Increases attack speed and speeds up motion of charged attack

For Both styles:

Smite corpus/grineer/infested – Increases damage against respective faction

Sundering Strike/Heavy Trauma/Jagged Edge – Increases puncture/impact/slash damage respectively

Fever Strike  – Poison damage

North wind – Ice damage

Molten impact – Fire damage

Shocking touch – Electric damage

Reach – Increases melee range

So those are the important weapon mods (not including crit builds). Also most enemies take more damage if you aim for the head.

Elemental damage:

I mentioned elemental mods earlier, each element is good for different factions take a look below. Make a habit of switching mods for the enemies you face (it tells you on the map screen which faction you're up against). 

Corpus – Use electric mods for more effective damage against these.

Grineer – Armor penetration mods to deal the most damage since most have armor.

Infested – Fire mods give the best damage

So pair these elements up with mods that increase damage against a faction. 

If you have enough space do put on a secondary elemental mod as that will also increase damage. I would recommend an ice mod as it slows enemies down on hit and is effective against shields. 

As of Update 11: Elemental mods can now be combined to provide better effects:

• Ice + Electric = Magnetic                      Reduces Max Shields
• Ice + Fire = Blast                                   Small Aoe Knockdown effect
• Ice + Poison = Viral                               Reduces Max HP
• Fire + Poison = Gas                               AOE poison effect
• Fire + Electric = Radiation                    Causes Confusion
• Electric + Poison = Corrosive                Reduces Armour

If you have more than two elements or are using a weapon with its own element then the priority for combination starts from left of the first row and then from left of the bottom row on the mod equipping screen for the weapon. Eg.

Since electric and ice mods are first two elemental mods in the order they combine to magnetic leaving fire by itself as heat. If the weapon had an element then the fire will combine with that native element.

This time the fire and electric mods are switched. This leads to Fire and ice combining to form blast and leaving electricity by itself.

Final Enemy weakness list:

So if we add these new element combos to the list of enemy weaknesses (bold being best) we get:

Corpus humans – Magnetic, Fire, Viral, impact, ice, toxin
Corpus robots – Magnetic, Impact, cold, electric, radiation, corrosive
Grineer – Puncture, Corrosive, Fire, Viral, blast, gas, toxin, slash
Infested – Slash, Fire, Blast

For the best dps you will have to potato your weapon but that can wait till you find a nice weapon you like and have more experience.

Warframe Mods

Every warframe has different stats and a different way of playing. They also come with all 4 of their skill mods when you build them. These skill mods can also be upgraded for better damage or duration,

Focus – Increases damage from abilities. Do not get it for warframes that have no damage skills like Loki.

Continuity – Increases duration of skills like decoy.

Streamline – Increases power efficiency so less energy consumption.

Flow – Increases maximum energy.

Constitution – Nightmare mod that Increases skill duration and helps you get up faster if you were knocked down.

Stretch – Increases the range of your skills.

Rush – Increases run speed of your frame.

Marathon – Increases stamina so you can run longer.

Redirection – Increases Shields

Fast deflection – Increases the rate at which shields recharge.

Vitality – Increases hp

Vigor – Nightmare mod that increases hp and shields

Thief's wit – The minimap will show nearby containers and resources as a yellow mark. Hopefully you won't need this once your used to what everything looks like.

Aura mods:

These mods can be obtained from alerts and give your warframe an effect as well as increasing the total mod capacity. Its best to get a matching polarity as it doubles the extra slots given. Level them up for increased effects and increased mod capacity.

Their effects also apply to the whole team and can stack, so make sure you get one ASAP.

Energy siphon – Restores energy to the team. Maxed it gives 6 energy every ten seconds. If your whole team has one that's 24 every ten seconds. Probably one of the best.

Physique – Increases max hp

Rifle amp – Increases rifle damage. 27% more when maxed.

Steel charge – Increases melee damage. 18% more when maxed.

Rifle/shotgun/sniper/pistol scavenger – Increases ammo gain from pickups

Rejuvenation – Restores team hp.

Shield disruption – Reduces enemy shields

Corrosive projection – Reduces enemy armor

Enemy radar – Shows enemies on minimap as red dots.

Speed holster – increases speed you can switch weapons.

Infested impedance – Reduces speed of infested.

Try and get any aura mod at first as something is better than nothing especially when you don't have much mod capacity in the beginning.

Sentinel:

These are floating companions that have their own hp and skill. Different Sentinels come with their own special skill mods and guns. At the moment there are 5 sentinels. The first four can be bought from the market place for platinum or built from blueprints that cost 100k credits:

Shade – Makes you invisible when enemies are near till you attack them

Wyrm – Can stun nearby enemies

Dethcube – Highest dps of the sentinels

Carrier – It picks up drops.

Djinn – You will need a clan in order to craft this from clan research. Its a fighting type that attracts enemies and stuns them for a short period.

You can also equip their guns the same way as you would a rifle with some exceptions. Sentinels do not run out of ammo so you can ignore adding any ammo mods. Also they have 0% crit so no need for crit mods either. 

Best to add serration, speed trigger and other damage mods of your choice.

Mods for sentinels:

Coolant leak – Slows nearby enemies down

Guardian – Sentinel charges your shields up

Regen – Sentinel revives when it dies. It recovers more hp the more you level this up.

Sanctuary – Puts a shield up when you try to revive an ally

Spare parts – Has a chance to drop rare materials when sentinel dies and cant revive. 45% chance when maxed

Vitality – Increases sentinel hp

Steel fiber – Increases sentinel armour

You may have noticed that I left out the corrupted mods. That's because those mods can only be obtained from the orokin derelict and need a well equipped team. You can purchase the blueprint key to enter in the market, it uses nav coordinates which are those black orbs you may find in containers. Also every corrupted mod gives a negative effect as well as positive.

As for crit builds it's best to wait till later in the game till you have access to better weapons. Generally sniper rifles and bows have a good crit rate making them viable for crit builds. However they have a slow fire rate so make sure you have an aoe melee or fast secondary in the event you get swarmed.

>> Recommended Path

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