I use VS2005, VS2008, VS2010, PHP, ColdFusion, etc. on Windows 7 SP1. For some reason, the .NET 3.0 or 4.0 Handler Mappings were not listed on my IIS Web Sites (including the Default Web Site) but they were listed on any new Web Sites that I created. I tried various combinations of aspnet_regiis.exe, ServiceModelReg.exe, uninstall/reinstall of .NET, and so on but none of them worked. What finally worked was simply this:
Launch IIS Manager, select the Default Web Site (or other web site having this problem), open Handler Mappings, click Revert to Parent.
Before doing this, you may want to examine the Entry Type column of the Handler Mappings view to see if there are any that are not Inherited, since those might be related to the product that disconnected inheritance in the first place. One thing that can disconnect the inheritance is changing the order of the handlers.