[gregmac]

How does this work with apps?

Many spew entries all over the registry (adding stuff to startup, context menus, special icons, etc), and it seems like those entries are also often responsible for the issues in the first place. Keeping those across a clean install seems counterproductive.

Likewise, installing the latest version of all the random apps is probably going to help more than hurt, and that's just as likely the actual thing that "reinstalling windows" fixes. If it retains older versions you lose that benefit.

All of this is ultimately bad software. If software can get a different state by installing fresh than it does going through the upgrade process, it is broken. (This includes the OS.) Too many vendors just don't care though, or have figured out it's more profitable to make their users do a reinstall than actually make their software not suck. This applies equally to the OS as it does to every app.

For like 99% of apps it's not even that hard to do it right, it just takes a tiny bit of knowledge, effort and caring.