Stalkers

My favorite is a 5S, due to the hardpoints and the option for 2 AMS systems--highly effective. Otherwise, a 3F, due to hardpoints and an extra 25-30° of twist. This is the one you see the most and it's the easiest to get used to, due to the twist.
Not a whole lot of difference in what I run, just slight variations of LL/ML, SRM/SSRM. Mainly just a matter of figuring out the best layout to cram in the weapons, group tight and run the lowest heat possible. Hardly rocket science, but here you go:

The 5M isn't bad for packing a punch and managing heat well, but not the best hardpoint layout IMO. This is my bread and butter build, the idea I start with and then make minor changes. Also, probably the easiest to run heat-wise until you get your perks doubled after mastering the class. Same build can be pretty much applied to any variant, just not with as nice a fit.
Stalker 5M: 4LL, SRM4 SRM6
Heat: 1.32
FP: 51
Armor: 496
Groups: 1: left 2 LL 2: right 2 LL 3: SRM's
Gives a nice punch from the SRM's, and in this build there are no missile doors to remember to open, the SRM's are stacked to save space and you get all the DHS's you can fit with no wasted space.
Drawback: STD 280 is a little slower and less heat efficient than a 300, but again, you get more DHS's.
After this, no reason to go with a 5M IMO.

My favorite 5S builds:
Stalker 5S: 5LL, 2 AMS
Groups: 1: left 2 LL 3: right 2 LL 3: torso LL
5 vs 6 LL since you can maintain fire longer mixing in that single shot 3rd group. Less alpha, but more damage in a drawn out fight. Dual AMS.
Light on armor, but only in the areas you rarely get hit in a lot. Stalkers rarely get much damage to the legs, no one has time to worry about that. LOL
Simpler, but does a lot of accurate damage.
Uses a STD 300 engine, what's in most of my Stalker builds.

Stalker 5S 3ML, 2LL, 3SRM's
I keep changing this one around. Sometimes as it is here, 3ML, 2LL and mixture of SRM4/6, other times I've got 4ML(arms) and 2LL(torso) and move the SRM's around. Good starting place if you want to run more SRM's. Dual AMS and 300 engine.
*Right now I've got this with 4ML, 2LL, 4 SSRM's with some promising results, especially for taking out the lights.


3F main build:
Stalker 3F
More of the same, but on the twisty platform.
4LL 2xSRM6
300 engine
*Currently I've swapped the SRM's for 4 SSRM's on one of my 3F's.


If you're good with heat (1.17), here's the big alpha (68):
Stalker 3F
2 LL
4 ML
2 SRM, 2 SRM6
Really not that bad with heat until you unleash the SRM's. Might want a coolshot with this.
Groups 1: 2LL (torso) 2: 4ML (arms) 3: SRM's


I don't bother with the other Stalker variants, I don't care for the hardpoint options. I like having 2 3F's and 2 5S's at the ready with the slightly different layouts and I keep the one base 5M build as the best general purpose build that I don't ever alter.


Update:
Misery

MISERY