Assuming that you're running it from the same directory the .csproj file exists in (using Visual Studio 2005 Command Prompt):
msbuild wapProjectName.csproj /p:Configuration=Releasemsbuild wapProjectName.csproj /target:_CopyWebApplication /property:OutDir=c:\SomePath\ /property:WebProjectOutputDir=c:\SomePath\ /p:Configuration=Releasecopy bin\*.* c:\SomePath\bin\
Enjoy.
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