First and foremost, I like Mart's Mutant Mod, he is, I believe, to FO3 what Darth Vador is to TW. I also like Road Wardens,Alternate Start, Wasteland Travellers and many others.
I absolutely agree about Mart's Mutant Mod.
FOOK2 is a great addition to weapons and armor. Also adds some nice tweaks to combat and some new possibilities.
Mine is tied between Fallout 3 Reborn and Wanderer's Edition. I'm a realism nut when it comes to shooter/role-playing games