Wow, it's been a long time since I thought about this, but meh I still have some ideas.

Basically I'm thinking of starting work on a strategy game with persistent elements. I've made some changes to my original idea (which was very ambitious) but anyway.
Each player has their own main base which cannot be attacked by other players. Each base contains things like research buildings, workshops etc. and serves as the starting point for the game. Players would select an area to attempt to invade from their base (I may have this space-based so that players can 'hyperspace' to any location on the map) and these areas would provide a steady income for them until they were captured by someone else.

My other idea is to have players join a 'lobby' which would select players of even(ish) skill and pit them against each other, with the winner taking some extra resources for their main base. This means that I can ignore the distance between the areas and have a more modernish game which I'd prefer. The main base can provide support such as artillery and air support which would also be cool. The advantage of this is that I wouldn't require a dedicated server to keep track of who owns each territory - I could fetch bases from a central database when players log in, serve the battle on one of the player's computers and then post the outcome to the web-based database. This would also allow cool stat tracking sited which, frankly, I'm obsessed with.