I run a Minecraft server with/for a small-ish group of friends and family (~25 people whitelisted). The problem we've faced is that as Mojang adds more features, you have to do a reboot of your map if you want to have access (or easy access, I should say) to them if you're playing in Survival mode. Because of this we've already rebooted once, since we ran one map from ~1.2 beta through the 1.0.0 launch (to get NPC villages, Fortresses+The End, etc), and now are facing a second reboot because of Emeralds being added (and to get a map with jungles not out in the far away/unexplored areas).
Some people wanted to keep working on old projects or at least have access to them, so I found a mod called Multiverse that allowed me to set up portals across worlds. Now our old map is Creative / free build, our current map is Survival, and we have a flat map in Creative for large projects. When 1.3 gets released we'll probably spawn a new map and change the current map to creative (with its own inventory, separate from the new map) and start a new.