I set Dogmeat to "stay" outside the control door in the rotunda while I was doing all the stuff in the basemant and I thought I'd unset him when I escorted the doctor through the tunnels but I hadn't. Now the Jefferson Memorial is inaccessible and I can't get to him.

Will he just go back to V101 or can I use a console command to retrieve him?

Maybe he'll return to V101, but if you want to try console comments:

prid 6a775
moveto player

http://fallout.wikia.com/wiki/Gamebryo_console_commands
http://fallout.wikia.com/wiki/Dogmeat_%28Fallout_3%29