Trekmovie.com has compiled a list
of all the inside jokes, Easter eggs and other references in the J.J. Abrams Star Trek movie. R2D2 even made an appearance in the film -- which we totally missed.
R2-D2 LOCATION ANSWER (**SPOILER ALERT**)
During the Drill Machine sequence as the Enterprise comes out of its barrel role amidst destruction of the other Federation ships above Vulcan, we cut to an interior Enterprise bridge over the shoulder of Kirk that is looking out through the front viewscreen. In space, R2-D2 is floating in the debris from about the top middle of the screen to the bottom right.
See the rest of the list here. We did catch most of those, but not all.