Navigate to your Programs menu > Microsoft Visual Studio 2005 > Visual Studio Tools > Visual Studio 2005 Command Prompt.
this command prompt has all the necessary .NET environment variables set for the the command line session. You can change directory to your solution directory (e.g. c:\projects\mySolution) and run
Msbuild.exe mySolution.sln
You can see the various options available using msbuild /?
Msbuild is located at C:\Windows\Microsoft.NET\Framework\v2.0.50727
On top of msbuild /? quick-option check, you may reference the MSBuild Command Line Reference page for more explanations on its usage. And how to build specific targets in solutions.