Google has released an official gmail notifier, which is good. There were a few unofficial ones bouncing around, but I couldn't get any of them to work well so I gave up. I'd rather have one that won't break anyway, straight from the source.

Instead of folders, gmail has labels. You can configure filters to automatically label a new email when it arrives based on subject, sender, etc. I use this for mailing list emails. Unfortunately gmail notifier does not see new labelled emails, only new unlabelled ones that appear in your "inbox". Why is that?