Sometime last year, when we migrated our Win 2003 + IIS servers over to 2008 + Apache, I ran into an issue. It only happens on 64bit Windows (and 2008 at that), and it just slipped my mind to blog something on it. It came up again on a list I follow, so it appears to be a good time to blog on it. I also got transitioned away from the server team over to the development team and the desire to post about it also went the ladder of "things I need to do".
The error message is "The application has failed to start because its side-by-side configuration is incorrec". I noticed that the machines I DIDN'T have an issue with already had .NET 3.5.x on them. The machines without it, this error cropped up. The solution (for me) and for the poster on the board was to simply install .NET on the server. After that, no more issues! Another suggestion was to install the VC 2008 components from Microsofts site. I've yet to try that, but it may work.
The other issue I ran into is after getting everything all hunky dory and working, the Apache connector just downright fails as soon as the 9.0.1 patch was installed. The solution there was to run through the wsconfig connectors immediately after installing ACF, THEN do the upgrading of the various servers and instances.