To get slightly better performance from a VNC server running on a Mac OS X machine, run ShadowKiller. No shadows means fewer updated pixels, and the ones that do change are more easily compressed. Presumably running some kind of theme that has less translucency than Aqua would help even more.
Even if Mail.app is set to remove messages from a POP server "right away" there's some circumstances in which they will be left there indefinitely. Specifically, if you have a rule that auto-deletes certain messages (say, to remove high-scoring spam messages) then Mail.app fetches them from the server, checks them against the rule set, discards them, but forgets to also remove them from the server. Until this bug is fixed, my workaround has been to modify the rule so that it just moves those messages to the Trash and marks them as read. This does mean that I have to remember to empty the trash periodically but 1) I do that already anyway and 2) it's better than ending up with 40,000+ messages on the server and having my webmail client and other not so robust programs die.