[TECH SUPPORT] I had problems with Apple Mail 2.0.7 hanging. Wouldn't let me quit (I had to Force Quit), and stopped sending my junk mail to the junk mail folder. Wouldn't even recognize my previous recipients.
Turned out the problem wasn't really Apple Mail's fault. The problem was that the mail server on one of my mail accounts wasn't operating properly. It was glacially slow, but not slow enough to time out. The reason Apple Mail wouldn't quit was it was still trying to download mail from the bad mail server. The reason it wouldn't send junk mail away was that it waits until all the mail is downloaded before doing so, and all the mail was never downloaded.
Now that I have disabled that particular mail account, Apple Mail operates properly. Tragically it's my "@craftyscreenwriting.com" account. But what can you do?