yeah, its mostly personal preference. i mean, most units within a certain price range are pretty close in features (and most of the essential features have already been mentioned here.) and like lee said, pick a couple that you might be interested in and pick your favorite one.
i think pretty much, price will dictate the group of units you select, then available features will narrow it down some more, then you pick which ever one you like the looks of and controls and things like that.
when i picked mine last week, it came down to a double din unit with some basic features, or a single din unit with a TON more features. i also considered the aiwa cd-mp32 (or whatever the better mp3 playing unit they make is) and i looked at a few others that play mp3s (i think its a cool feature), and i ruled all of them out; that came down to personal preference - i didnt like the looks of any of them, and none of the ones i saw had user friendly controls.
some brands are also known to be not so good, while others are known to make great products, even the lower end models, so thats another thing to consider. oh, and, also, your plans for the system. for instance, if youre not planning on running any amps, then dont worry about preamp outputs, but if you want amps, you better make sure your unit has preamp outputs (or enough of them) - you could just have one set of preamp outputs, and run everything off of an electronic crossover, but, well, once again, personal preference.