I'm looking for a tool that will generate an assembly/project dependency diagram in Visio (or as close as possible) to assist me with breaking up some of our system into more manageable trunks.
The ability to include/exclude non-project dependencies is a must (i.e. include/exclude System. assemblies).
Visio has the ability to reverse engineer UML from your solution. You can find more information here. It's not clear to me whether you can include the .Net assemblies, however -- since they are not really in your solution.
Try ReSharper. (I'm not associated with the product or company, but it provides many nice features for dependency walking).
You can also try the Depends.exe with the SysInternal toolset - now from Microsoft.