Punkish made the suggestion in one of the comments (actually the only comment) back on May 29th about adding an actual database to SQLEditor and turning it into a database program. The more I think about this the more I like the idea so it may end up happening. Although it will be a separate program from SQLEditor. SQLEditor will continue as it is because I need it that way for various projects myself.
BTW: The new cocoa version of SQLEditor is about to be released into public beta. Probably either today (Sunday) or tomorrow (Monday).