Check windows add remove programs, as .NET framework should be listed, you may even have more than one version listed.
Based on your list from C:\WINDOWS\Microsoft.NET\Framework you have it installed and are likely to have multiple versions listed in add remove programs.
However, I wouldn't recommend removing anything as without doubt this is the most confusing can of worms, some programs requires certain versions of .net and it is very difficult to even find what programs on your system even require it, much less what version it requires.
The latest .net version 3.5 doesn't act like in the case of an OS SP roll up old versions and as such doesn't appear to be backward compatible or you wouldn't need to retain the .net 1.0, 1.1, 2.9, 3.0, etc.
As I said a right royal can of worms.