If you ever installed asp.net 1.1 over 1.0 you will know that it changes all the mappings in IIS to 1.1. You then have to run aspnet_regiis -i to correct it on the sites you want back at 1.0. That's fine but it is a bit of a hassle.
And with Whidbey and .net 2.0 available as a technology preview in MSDN downloads, you will need to be aware of the same issue. When you install it all your sites will become mapped to asp.net 2.0 You can correct it again with aspnet_regiis, but there is a cool little utility from Denis Bauer at http://www.denisbauer.com/NETTools/ASPNETVersionSwitcher.aspx that makes this a breeze. Well worth a look.