You tend to be running a program in memory once you've loaded it from the hard drive

As for stuff getting left behind in the registry in windows when you remove a program. You can blame that on the people who made the program for not doing a very good job with the uninstaller.
There's no reason why quicktime 3.0 still needs to have a record in your registry after it's been uninstalled for conceptionally, years.
I'm sure that many of you know what happens when you install/uninstall many applications on Windows...it generally gets slower. So is there a program that allows me to virtually install and run an application purely from memory w/o using the HDD? Or perhaps w/o writing to the registry? Something like a container program?
You're **** out of luck. Just get used to cleaning out your registry i guess. With the registry in windows, it's just something you'll have to get used too until microsoft does the right thing and gets something better in place of it. Or don't use windows. The virtualization solution in this thread is unnecessary. The portable apps one is better. But, really, why do any of these?
Clean out your registry. It's pretty easy. Solutions that make it easy have been mentioned.
Clean your registry, if you're too defiant for doing it, then you suck at windows and computers.