I recently came across an issue where Coda and Transmit would just appear to hang when deleting files on my local machine. Fortunately, the good folks at Panic were able to identify the issue. Turns out, it's a OS X bug.
Here was their response via Twitter:
It's a bug in Mac OS X. It affects a lot of seemingly unrelated things. We're hoping Apple fixes it shortly.
The workaround is to run this from the terminal:
sudo killall -KILL appleeventsd
I'm posting it here because I keep having to hunt for it every time the issue comes up, and there are bound to be others that need it. For more details on the bug, check out this post.