There are a lot of things that require the .NET framework or at least one of it's flavors. The ATI/AMD graphics drivers are one example. They require .NET 2.0 for the Catalyst Control Center to run. You used to be able to get away without installing the CCC, but now they've added the Catalyst Install manager which also requires .NET.
My advice is to only have the versions installed that are needed by installed applications or those that are installed as part of your particular version of Windows. I do not have v4 for example because so far, nothing has told me that it needed it. I would agree that you should not uninstall any .NET versions that you have.
The Media Center portions of Windows also require .NET. Even the separate Media Center of XP required v 1.1. Only XP Home or Pro do not install nor need any form of .NET in a fresh install. XP media Center (1.1), Vista (3.5), and W7 (4.0) come with .NET embedded into the OS.