The E46 has the computer (mpg, range etc) more integrated into the guages. I personally think it looks more modern than the, imo, boxy E36 variation. Thier still the same engine (minor difference) the the E46 wieghts a bit more. If you know how to drive stick, get the E46 in manual. If you want to save money, get the E36. Both will have problems, mostly based upon how they were treated in the past. Just have them both checked out before you buy either or. My vote goes to the E46, because I drive one, appreciate it's looks, and like the smooth feel of her interior, etc. But I'm also extream low on cash after getting my 328i.
Drive them for yourself. If both are stick, or both are automatic, you'll notice that thier relativly the same +/- a fraction of a sec, only appearence would dictate anything otherwise.
Though I must say that while getting an E46 would look imo, more aggressive, the E36 has more available aftermarket accessories.
To answer your question more specifically,
0-100km = 0-62mph
1999 328i (E46, 4 door stock) 0-60mph, 6.9sec. 1/4mi 15.2sec
1998 328is (E36 2 door coupe) 0-60mph, 6.2sec. 1/4mi 14.7sec
1996 328i (E36 4 door "sport") 0-60mph, 6.4sec. 1/4mi 15.0sec
I don't know if these times are under optimal condition for each.
I've attached two comparision pics, from the same site. Both M3's. They're the only ones i could find that would be the least biased toward each other:
Stability, well that I really can't answer, my 328i handles VERY WELL, though I've also got a sport suspension set up.
I hope that I've given you some of the information that you wanted. Remember that getting an E36, will be cheaper to buy as they are older and most likely will have higher mileage. And vise versa for the E46.