Merlin mentioned a plug-in for Mail called Mail Act-On a couple of days ago, and I just got around to trying it out; it's great. Like many people, I used to use the trick of appending three underscores followed by the name of a key combination to an Applescript's file name to allow me to trigger it with that key combination. So a script called 'Flag items_ctl-f.scpt' would get triggered by using the Control-F hot key. Unfortunately, Tiger broke this little wheeze, and I was getting fed up of having to drag and drop to file messages.
Act-On lets you create specially named rules in Mail which perform actions and can be triggered by a key combination. Even better, if you press the special Act-On hotkey (` by default), it brings up a Quicksilver-like bezel which lists the keys and actions, so you don't have to remember what activates your 'File in Project X mailbox' rule. It's actually much more convenient than having to create lots of separate Applescripts, though if you want to do something that can't be accomplished by a Mail rule, you can still use the interface to call an external applescript.
If you use Mail, it's well worth giving it a try.