Plugin Alliance: Go to the website, log in and then authorize your computer. That's it. Plugins install to one folder. You want to uninstall them you just delete the .dll.
Native Instruments: Install their manager. Install whatever plugins you want to. Do a search for NI on your hard drive and see how many folders all over your hard drive you find their crap.
iZotope: I never had any problems before but then I started finding massive files hidden deep which are supposed to aid in communications between their different apps.
Can't be more specific than that but you'll see what I mean if you try.