I am updating to windows 8 as I write this. Or more so, dealing with the fallout of updating earlier today.
The purchase and update went fine, but the first time I restarted after the update completed, somehow it got corrupted and I had to do a refresh. Which unfortunately, involved deleting every application on my computer (although non application data was not effected). I tried every other means I could think off, but windows wouldn't start at all.
So now I am in the process of reinstalling everything. Luckily I run a constant backup to a networked drive.
The only two programs the installer had an issue with were my virus checker and zonealarm, both of which I uninstalled beforehand.
The only minor issue I am having since I got past the corrupt install, is that the mouse seems to not work as smoothly anymore. Moving folders is a pain and sometimes folders/programs open with one click instead of two. Also using the mouse in the metro interface is a pain. There are unintuitive delays required in the motions to move tiles and close apps. Possibly to prevent you from doing it by accident, but it takes some getting used to.
All of the programs I have reinstalled seem to work fine, but I have a ways to go before I can say they all work.
I did try the app store. You need to have a windows live account to download even the free ones. I used my xbox account, but had to go through a ton of email verifications and password resets since my computer was no longer recognized.
I would definitely recommend doing a full backup to an external drive before you upgrade and set up your email first, because you will have to use it to set up a windows account.