Here' a few I use (they all came from fallout 3 nexus):
MARCO realtime stimpacks - prevents you from just pausing and using as many stimpacks as you want, now you have to use them in real time and there are side effects, makes healing much more tactical.
Amplified Crippled Effects - makes crippling various body parts more debilitating, so it now has very noticable effects on both you and enemies, making crippling enemies much more useful.
Deadly radiation - ups the power of radiation, because otherwise radiation doesn't really have much effect.
DK bullet time - Gives you a key to trigger bullet time that uses VATS energy - nice.
Accurate Assault Rifles - ups the awful accuracy of the assault rifles into something that's now actually worth using at medium ranges.
Better Frag Grenade Physics - stops the frag grenades from bouncing like bloody tennis balls and makes them behave more like a real grenade, makes grenades more useful.