I would go with the E46 328Ci. I have a lot of experiance with the 2.8L (M52) as it powered my E39 528. Great engine, and through a function of shorter gears and less mass the E46 is a lot quicker. 80% peak torque (206ft-lbs total, so about 180ft-lbs) at only 2000rpm thanks to VANOS, and it screams all the way to redline.
I think if you got the 323 you would be wanting more power right off the bat. The 328 gives you more stink from the get go, and since both are modern BMW engines, both cost about the same to mod, but the M52 has more power to begin with.
I love the E46 330, as I have driven them in SMG and 6spd with the performance package. However, the 328's cost a lot less, and there is some easy power to be had by going to Dinan, RMS, Active Autowerke (sp?) and many others. Not sure if Evosport makes any mods, but they tend to be cheap while holding good quality.
IMHO, get the most powerful engine you can afford, as the gains will go higher in the end, and you have more power till the mod bug hits hard. Just be careful, as mods for BMW's can tend to be expensive, but in the end well worth their cost.
Oh, I dont think I need to say this, but be sure it is a stick. Most BMW I6's dont mate up to autos well, as although they make good torque, the torque converters are a little loose and tend to water down performance a lot. The only exception is the E60 530 auto I drove, it seemed to do well.
Here are a few links to some sites you might enjoy thumbing through:
http://www.dinancars.com/default.htm
http://www.racemarque.com/rms_bmw/
http://www.evosport.com/home.html
Hope this helps at all. You know, for the price of an E46 328 you can also find a E36 M3, and with a little help by active autowerke you can have a nice turbo setup and be on the way to ongoldy 1/4 times. But, in the end, I think any of the 3 series line after the E30 (except the old E30 M3...those are gems) will treat you much better than almost anything thing else you can buy.
:cheers: