I realize this is a subtle feature, but I think it would be a big help.
Each time Transmission starts, scan the trash and make sure that you delete any torrents that have been moved to the trash in the finder - without Transmission running. Sometimes I like to delete a move file when Trans. isn't running. Then, when I restart, it re-starts all those things I just removed. Bummer. Just add some quick code to scan the trash to make sure that the file it's about to re-start hasen't just been moved to the trash. If it has, just delete the torrent quietly. Waaaay cool. I'll be so impressed if this happens and I'll recruit you programmers to the next huge like project I'm involved in.
Rock on!