I would recommend you minimize the impact of the conversion wizard by following this procedure.
1) Make a copy of your existing solution file (i.e. to have VS2005 and VS2008 version of the solution file, e.g. MySolution.sln and MySolutionOrcas.sln)
2) Open up the new solution, and choose not to convert any projects in the solution
This means you will be able to develop using Visual Studio 2008, and Target .NET Framework 2.0, but still be able to use Visual Studio 2005 (if required), or if other project members haven't moved across to Orcas yet.
Finally this method should also work with TFS meaning, you can develop with Orcas but your build server will know no better (I haven't tested this yet, but I'm pretty sure it will be OK as I have tested it with msbuild)
If you run into trouble you can do it manually:
For each project file in the solution change the first line from this:
<Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003" ToolsVersion="2.0">
The important part is the ToolsVersion="2.0", this will mean that VS2008 will not attempt to convert this project, and will target framework 2.0 for you :)
Finally once you have modified all the project files, you can open the new solution file (MySolutionOrcas.sln) in Visual Studio 2008 (Orcas Beta 2)
You can now allow Orcas to convert your solution (and it will not attempt to convert any of the other projects to Visual Studio 2008)