I ran across a known bug in MSBuild in Whidbey beta 2 that caused me considerable headaches today. It seems beta 2 will not copy project references to the bin directory of web projects when compiling with MSBuild. This issue will be fixed in the final release, but I thought some Google juice might help someone else find the definitive answer with less frustration than I had. Here's a relevant forum post on the subject.
In the meantime, I'll simply add a copy task to copy the relevant assemblies to the bin directory.
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Disclaimer The opinions expressed herein are my own personal opinions and do not represent my employer's view in anyway.