Simply installing VS2008 Service Pack 1 will fix the problem, if it's an error where the Debug CRT is totally missing from the sxs folder.
I had this happen to me with a fresh install of VS2008 on 64 bit Windows 7 and a solution containing a VC++ project. The debug build would crash when the C++ assembly was loaded at runtime, with a side-by-side error.
On Vista and Win7 (but not XP) the SxS error gives details about exactly what assembly it tried and failed to load - in this case it was VC90.DebugCRT 9.0.22.19. I checked the (embedded) manifest for the VC assembly and sure enough, it included a reference to this assembly and version.
Checking the sxs directory (%System Drive%WindowsWinSxS) showed that there was no VC90 DebugCRT installed in side-by-side at all! I had installed the VC++ runtimes, but these don't include a debug runtime. VS2008 is meant to install a debug runtime, but it wasn't there.
Turns out the original release of VS2008 doesn't install a 64 bit VC++ DebugCRT, but installing SP1 does. Once I'd done this, no more runtime exceptions and side-by-side errors.
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