Are there any guidelines or recommendations for managing libraries that aren't on nuget along with the packages that are.
Most of these may be 3rd party libraries that may never go on nuget unless we specifically put them on.
Is it best to keep these dlls out of the same folder that nuget uses to store its downloaded dlls or is it better to keep them together?
We would be looking at moving to DVCS once we sort this out and would probably add an ignore file to ignore the whole packages directory (and possibly add exclusions for these non-nuget dlls or just force them to be checked in if they ever do change).
My Personal Preferences (In Order)
For 1 & 2 i would recommend using Restore Package on build rather than storing it in your source control.
I'd also highly recommend against referencing any 3rd party controls from install folders or the GAC.