I forgot to lower the bass in my car, but I did try something else. I connected the speakers to my Windows box. The same song in iTunes sounded a little different, but that was to be expected with different speakers. I made sure the EQ was as similar as possible in both iTunes apps. I still don't know... it's hard to tell. However, I did play Half-Life 2 with the speakers and they sounded fantastic, even at half the volume (that's pretty damn loud too).
So then I connected my other speakers (previously on my Windows box, but up for sale on eBay now) to my PowerBook. iTunes sounded similar, but these speakers did sound better in Adium. The sound effects sounded much clearer and not muffled like I explained earlier. I wish there was a treble dial on the speakers' controller, but there isn't. Is there some kind of app for OS X that can increase the treble universally (i.e. for everything within OS X and not only iTunes)?
So I guess I'll be keeping the speakers. I think I'm just being overly paranoid about it. 😛 Thanks for all the help!