Animations: when to use them.

Short answer: never. Long answer: for the love of (insert sacred being/object here) don't ever.
In all seriousness, fancy animations have only a few legitimate uses in webcomics.

Animated GIFs bring up several problems. Foremost, they won't be seen by every reader: thanks to frequent abuse, most browsers now allow you to disable them. Fine, you say, I'll just write javascript to swap images! works great...until you find someone, tired of right-click disabling and dialogue box abuses, that has disabled scripting. If that wasn't bad enough, you don't control when a GIF begins its animation cycle. Even worse, the bandwidth cost is much larger.

Flash has been gaining ground in web animations, though it will chew up just as much bandwidth (or more) than an animated GIF. Browser settings to stop Flash Objects exist, though they are less prevalent as those for GIFs. Also you're betting that their Flash Plug-in is compatible with your authoring program--not the best place for your money as we've seen with version 8.

And what does Flash provide that you need? If used to display archives, it just makes it harder to save them or bookmark the page. If the comics themselves are animated, why not go all the way to a flash cartoon? If you're just using it for a 'next frame' button, that makes it harder to view the comic as a whole or reread previous pages, not to mention the slowing effect on reading speed.