this by no means is a complaint but I couldnt help but notice a few batman references or "borrowed" ideas. IMO javier bardem's character had similarities to joker, He was a bit crazy, laughed to himself and deliberately got caught and escaped. Also when bond and M were switching cars she said "this is much less inconspicous" I couldnt help but be reminded of Alfred when he said to Bruce "a lamborghini, much more subtle". Finally M's poetry speech she gave reminded me of the whole "darkest before the dawn" speech by Harvey Dent. Again, not a complaint, just things that caught my attention.
There are a whole lot more:
Both are orphans
The priest hole is also reminiscent of the Batcave
Javier giving the gun to M reminded me of the Joker giving the gun to Harvey Dent
Kincaid = Alfred
Skyfall Mansion = Bruce Wayne Manson
I'm sure there are a whole lot more.. some more subtle than others.
the orphan thing was from the original books, and thus isn't really a reference. Also Kincaid seemed much more like a Henry Jones Sr. type than an alfred type