These are the most popular maps, in order. Its the best stats database I could find. If someone has any other data please post it!
http://tf2stats.net/map_list/
We don't need to limit ourselves to these, but, for a fledgling server getting players in is the most important thing. The first page are the maps that bring people in.
I think the best setup is to use those maps as the backbone and have a few interesting but playable custom maps to keep things interesting/keep people around. By playable I mean they have to work with a full server. TF2 is stalemate friendly and a lot of times the cool/interesting seeming maps are actually a mess. I know that goes for my beloved Rats_1337 in csgo. We need to remember that the maps we like aren't necessarily the best bet for a fledgling server.
I think cp_balloonrace is a lot of fun as a breakup/fun/different map.