Lots of different packages are available - cold weather package, premium package, sport package, performance package on newer 330's, and many other options are available as well. Nothing's standard on a BMW! That's pretty high level - is there a more specific package your looking for?
Yes, the 2.8 liter has rated at 193 HP/206 ft/lbs vs 184/175 in the 2.5 liter (those are 325 #'s - the 2.5 liter in the 323 is rated at 170/181). HP is similar, but torque goes way up. Worth nothing, the 1999 and 2000 cars (323 & 328) have manual throttle cables, while the 2001 + models (325 & 330) have drive by wire. 2 totally different feels.....
If you looking for a car to modify, it isn't easy or cheap in a E46.