Is there a way to specify the order which Ubuntu tries APs I notice after moving around a bit I have a lot of extra AP's some which I use more than others I'd like to push some to the top of the list instead of waiting for a weak hot-spot to fail first.
Network Manager will automatically try to connect to the strongest signal that you have selected to automatically connect to. You cannot change that logic.
What you can do is to prevent less-frequently-used connections from connecting automatically, which should be fairly close to what you are asking for.
On Ubuntu 13.10:
Network Manager's layout changes from time to time, but the option is always in there somewhere.