A few of my favourite mechanics actually come from you guys (Crafty that is, not the forum - though the forum has produced some pretty amazing stuff).
In no particular order (beyond "as they come to mind"):
Action Dice: I port them to every other system I run now if they don't include them at default. SC was my first system with them and it was like magic. Awesome work guys, truly.
Narrative Control: Heaps of systems do it different, and do it well. FC has some good Narrative Control options and I'd like to see them expanded upon more in future. Dresden Files RPG (which I've started reading because a HMJesus is gonna run a game) has some utterly brilliant stuff for this.
Stargate's Core Gear rules: I prefered this to SC2.0 immensely. In Spycraft 2 you could be unable to get essential gear because you don't have the right pick types, which means the GM had to give them to you (and by RAW, penalise you for having to do so) - not a great situation. I actually saw a player take a Proteus Modified Dossier because they couldn't get one normally (which is hilarious, but terrible).
Spycraft 2.0's Personal Possession Rules (and by extension, Stockpile
): Brilliant. You have a set level and can get what you need/want. Faceman needs a bazooka? No problem - none of this "resource pick only" BS.
GURPS 4E Firearm rules: Aim action benefits based on the actual accuracy of the weapon (so aiming with a sniper rifle with match grade barrel and high end scope gives you much higher benefit then aiming with a smoothbore sawn off). Recoil values determine the difficulty of multiple hits when burst/automatic firing (putting 3 shots with a laser with zero recoil on target is substantially easier then with something that kicks like a mule). GURPS's firearm and tactical combat rules have it dangerously close to becomming my go to RPG for modern games - if I could take it's rules and put them into FC you'd have my perfect system.
Spycraft 2.0's grappling feats: FC's Wrestling chain pisses me off. The 2 tricks are just "pro wrestling" instead of actual wrestling. Spycraft did it right - Submission chain, Brawling chain, and Wrestling chain. You can make a wrestler rather then someone who piledrives people (which is almost impossible without them cooperating in setting up the move).
Varied attack types: Spycraft 2.0 had the "kick" attack, complete with it's feat chain support (Like). FC has a Kick chain, but only NPCs can gain Natural Attack: Kick (Do not like). It's not a problem so much as it is a logical disconnect (and I've actually had GMs not let me use the Kick chain because I didn't possess Natural Attack: Kick - because the RAW didn't support it). Other systems also have actions in place for things like Pistol Whip and Buttstroke, which I really like (and I can't count the number of times running SC2.0 that I've had someone ask what the rules for pistol whip/buttstroke are).
Location Injury: The Table of Ouch is a damn good start (though I don't like that your more likely to hit a key location because you do more damage). What I really
like is systems where getting shot in the leg is different (not necessarily better/worse - different) then being shot in the arm. GURPS has a good one, but it can get to be a little bit "too much" since you have to roll on it for every attack (and subsystems like armour are based on you doing so). I recognise that this isn't a wishlist thread, but what would move this concept from "merely like" to "love
" is if a happy middle ground between the two could be struck. Something like change the Table of Ouch to a table that determines location you hit and then produces critical injuries from there (in fact that's probably easy enough that I'm going to draft out a houserule like that today).
Improvised Weapons: Improvised weapons are cool, and totally fit the style of the genre - Bourne and Bond both use them extensively, so why not us? SC2.0 didn't (quite) get it right - spend an action die to find an improvised weapon? No thanks. Why can't I just freely decide
to use the chair the GM said was in the room a minute ago? The table was a little dopey too, but I really appreciate the intent.
Priest and Captain classes: My 2 favourite classes. Whoever wrote them should be proud of their work. Maybe not "technically" modern, but I'll allow it.