<p>I am trying to compile my apps (which uses 3rd party libraries) for the x64 platform. However selecting x64 from Build Configuration Manager from my VS2008 Pro doesn't seem to work. The binary does get created but my client wasn't able to get it to run on x64. </p>

<p>I wonder if the 3rd party DLLs could be the cause. Anyone has any idea on this?</p>

Do you have x64 versions of the third party libraries?  If not you are out of luck.  A process must either be fully x86 or x64, you can't mix and match libraries.  If the libraries are DLLs then you still need the export libraries from an x64 build.
In what way does selecting the x64 configuration in VS not work?
Updated:
If your app is .NET and architecture neutral, then it will be loaded as 64 bit on 64 bit OS'es.  However, if it relies on 32 bit DLLs then this will fail at run time. You can force your exe to always load 32 bit using the
corflags
utility.