We had the Top freezer/Bottom fridge before we remodeled our kitchen, then we went with side-by side (a really big one-29cu. ft). My DW loved our side by side so much that when we moved to the new house a few months ago she made me take the side by side with us, even though we had a brandnew Sub Z bottom freezer (which I love) in the new house.
Here's my take on the whole thing, it all depends on your food storage habits...
1)Top freezer is okay, but badsed on the options/features you can get (or more to the point can't get) with them I don't like them so they are last on the list.
2)Side by side - are very feature rich (i.e. beverage center/ice service in the doors, etc.), but they usually (unless you get a monster sixed one) can't hold big trays of food if you have any inclination to having a big party and need that kind of space. They are usuall a 1/3-2/3 split nowadays too. I like this most.
3)Bottom freezers/top refrig. - are very "comfortable" to use...think about how much more often you go to the fridge for something vs. the freezer it just make sense to not have to bend down to get something out of the fruit/veggie drawer since you will likely go there more often than the times you will go to the freezer. Alot of times though - especially with built-ins these don't have a great deal of depth. So they are # 2 on the list.