Wierd. If they're tiny black spots, they could be dead pixels on your monitor but dead pixels usually only show up one at a time, not many at the same time.
For scrolling,I'm not quite sure what you mean. If you click on the arrows on teh window and nothing happens, that could be one thing, whereas it you have a scroll wheel and it's not responding, that's something else. One thing ou can always do is to unplug and replug you mouse and see it it works properly then.
AS far as the black squares go,assuming it's not dead pixels, the only thing I can think of is to do an archive and install of your OS. Archive and install keeps all your settings, etc and just gives you a fresh OS. It usually availble on your install CD/DVD, if you click on the Options button. You can read up on Archive and install on your Mac Help.
Using OSX 10.3.9 on a G4
