In my opinion, there isn't such a huge difference except fuel consumption and exhaust note. The 330i is a lot thirstier than the 325i with my driving style. The 330i is quicker though, especially when you're not keeping to the speed limit and the torque on the 330i ensures that you need less gear changes. On the other end of the scale, the 325i feels and sounds smoother, revving to the limiter easier. It's a close call though. I've only had my 330i for a short time, but the exhaust note is addictive, even at startup in the morning. That alone is reason enough to get a 330i. The 330i also has a 6 speed manual box which is a huge plus and helps with fuel economy on the highway.
Comparing a manual 325i to an auto 330i is a different ball game altogether. The 325i M and 330i A is so close to call, it's not even funny. I used to have a colleague with a 330i A and I had the 325i M. From a standing start he could not get away from me (Neck in neck up to about 150km/h), but his fuel consumption was almost double that of the 325i. Not only is the 330i more expensive to acquire, you also keep paying more at the pumps. I say if you can get either in excellent condition, you should take it. BMW will stop making N/A 6 cylinder engines soon. So grab a piece of motoring history while it's still available.
I must admit on the open road at legal speeds the 325i is only slightly better on fuel consumption. In mixed driving the tables are turned drastically, and the 325i wins hands down. I must admit, I am a spirited driver though.
That's it, my 2 cents.