There were third party addons that did some pretty crazy things. I don't know if animations were among them, but I do remember at least one that would completely retheme windows with different shapes and layouts, Windowblinds I think it was called.
I definetly remember Windowsblinds too (and geez, it seems they're still around ...).
I was into LiteStep, which basically was a shell replacement for explorer.exe.
I'm also reminded how trivially easy it was to configure Win9x to use a different shell: you'd just edit system.ini under [boot] to say shell=litestep.exe and you were done.
Here are some screenshots:
[0] https://www.stardock.com/products/windowblinds/wb-aug00g.jpg
Fun fact, Win98 still had progman.exe installed (from win 3.1 and earlier). I had to switch to it in system.ini one day when something in explorer got corrupted and the normal UI wouldn't load.
http://toastytech.com/guis/cpdesk.html
It was bloated and unstable though, so I was glad to upgrade to windows 95.
I also used eFX, which was a free Windowblinds competitor that made it super easy to make skins, and released a ton of garish and ugly ones back in the day.