I messaged Jesse Hildreth, the ILM animator who was responsible for that sublime little dancing Groot at the end and he told me that Vin Diesel definitely did not perform mo-cap for that shot, and in fact it was James Gunn who performed it for the reference footage!
Jesse was also responsible for most of Star-Lord's helmet shots, some close-ups on Rocket's hands and a couple of Milano shots - all cool stuff!
UPDATE: Jesse just sent me a link with the following quote:
"I'm not motion-captured, but I'm motion-referenced and that is 100% me dancing..." James Gunn
Read more at http://www.comicbookmovie.com/fansites/MarvelFreshman/news/?a=105173#1ZQTzc6HS9QULsvb.99