My iPad has ceased to synchronise with iTunes - some error message pops up about some service or another not running (I've checked and haven't blocked any services). Reinstalling iTunes over the old installation didn't help, so now I want to totally remove the old installation first.

So what happens to the apps I have bought and downloaded? Do I need to do anything special to safeguard them, or are they all linked in to my Apple account?

I believe you can download anything you've previously purchased from the iTunes store again for free providing you're using the same account. So if removing iTunes also removes the apps, you shouldn't need to pay for them again.

I would back up your iTunes folder before doing anything.

Certainly in the case of music that you have downloaded you can copy the music back to the PC from an iPod but I believe you cannot download again from iTunes.
You also cannot copy your own music back from the iPod to the PC using iTunes..

Not sure whether it's the same with apps.

I believe that removing iTunes doesn't delete your media but I really wouldn't take the chance until you've got everything backed up.

Uninstalling iTunes wont remove your media. All apps are indeed linked to your account and can be downloaded again if need be. I don't think its the same for music.

Thanks for the advice guys... although the problem fixed itself before I got any further. A new computer is on the horizon though, so it'll come in handy soon enough.