Hard to say on those prices. To me they look average - not great, but not bad either. I think it depends on what area of the country your in too. In some areas that would be considered high, but perhaps not in LA? Check nada.com - it'll ask for your zip code and give you a ballpark figure.
I don't know the specs on the 3.5 SE, but I know it's faster than a 325. You might be disappointed in the 325's power? I recently had a 330 loaner and it definitely has more grunt. Not huge, but noticeable. Other than the increased engine output and bigger brakes (and performance package - see below), you can get all the same options on a 325 as a 330. Brand new w/ similar options, the 330 is ~7K more than the 325. I think it's personal opinion as to whether it's worth it. Used that price difference probably falls to 4-5K?
A bit harder to find is the 330 with performance package (often times called a 330 ZHP). It was offered starting in 2003 in a 6 speed, 4 door only. In 2004 it was offered with auto (steptronic) and coupe & convertible versions as well. It adds some nice cosmetic and performace upgrades over the stardard 330. Check out BMWUSA for more info.
Good choice on the colors - silver and black are my two favorites. They probably have better resale value than most other colors as well. Keep in mind there are two blacks out there - jet black and sapphire black metallic. They look very similar, but if your picky, you might like one over the other.
What would I look for in a BMW 3 series? In terms of color - silver or black! I prefer a manual, but it sounds like your set on the auto. More than anything, I'd recommend finding one with the sport package (17 inch wheels instead of 16, 12 way adjustable sports seats, sport steering wheel, sport suspension). I wouldn't even consider one without it. Xenon headlights are the other popular factory option. So, I'd recommend finding one with at least those two options. Cold weather package will give you heated seats, folding rear seats and ski bag. The heated seats can be found as a stand alone option as well. Premium package adds leather, interior wood grain trim, auto-dimming rearview mirror, and moonroof on the 325. Moonroof and leather can also be found/purchased without buying the entire premium package.
This has gotten long so I'll wrap it up. Good luck in your search - hopefully I've answered a few of your questions.