Currently I'm running the following mods.
Xrepair weapons lets you fix your weapons with scrap metal and wrench's. Truly a life saver.
Lawbringer Bountys (adds 1k in caps or more for bringing in proof that you have killed one of the top 20 bad guys in F3, List starts with Tenpenny and Burke and goes from there)
Regulator Hnew touches up the Regulator HQ a bit, adds lots of handy items.
Better Regulator Duster is another good one. Now you can wear the duster and still have armor.
(yes I like playing Regulator "good" characters)
LJD Enclave Enabled brings the Enclave soldiers into the game right away rather than waiting till you reach the point on the main quest. Be prepared, they are tough, nasty, and there is a cell of them not far from V101.
T3T Weapon Tweaks and AutoAim Companion brings a few of the standard and unique guns up a notch in damage and accuracy. Be warned, the same is true for the bad guys. I really like what this mod does for the Lincoln, and Ol Painless rifles. As well as the Reservist and Victory sniper rifles.
TheHideout puts a sweet garage with bed, storage, radio just outside Megaton.
Hidden below is a vault full of goodness, including a character that can repair to 100%, and 3 transporter tubes (Rivet City, HistoryM, and Little Lamplight) Its cool, its clean, has everything your wasteland wanderer needs.
Wasteland Revisted totally reworks the whole F3 economy. Stims are 1500 - 2k$ but are also more powerful. A single stim can take you from 20% health to 100%. Food weighs less, renames many items, almost turns F3 into a whole new experience.
ZableBlazes Companion Mod lets you turn any NPC you can have dialog with into a companion. Including companion equipment share, orders, etc.
These are just a few of the many I've tested. And these seem to work well with each other. Solid, stable, etc. Best mod single stop shop I've found is
http://www.fallout3nexus.com/downloads/categories.phpTake the time to sign up for a free account. Will let you download larger files, etc.
They do a great job there, can't praise them enough.
I especially appreciate their "Latest Files" quick to browse, and keeps me up to date on whats new.
I still have not really found a sniper mod that completely suits me.
ShykeMiscPack comes close with his 50 cal semi auto. Not as easy to hit with, but rapid fire and large clip make it easier to survive in hostile enviorment with max difficulty.
Snipers Bliss is worth looking at, but is a bit light on damage IMO.
Too many supermutants get back up and attack after a good head shot.