Why not give them to Bruce Wagner's "bitcoin firehydrant"? At least we'd get a nice publicity event that might be pro bitcoin for a change when a million people queue up for free bitcoins in NYC.
I think a lot of people who donated to a non-profit will object to the difference with what Bruce is doing. Holding on to the coins until the EFF comes off the fence would be best I think.
In the future it is likely there will be significant legal contention concerning Bitcoin. At this point the EFF is one of the first organisations which comes to mind which might choose to defend Bitcoin. Their position would be weakened if they held a large sum of Bitcoins themselves.
Very high level of signal to noise ratio in this thread, lots of thoughtful posts, how refreshing 
Yes, how odd. I didn't like the trolls but now that they're absent I find myself missing them.
Exactly. Also, how would defending the existence/legality of a currency they've received a large number of donations in effect their nonprofit status? I honestly don't know but I could see how accepting this could be perceived as a big conflict of interest and weaken their ability to help Bitcoin in its inevitable hour of legal need. Any sort of donating the Bitcoins to something EFF believes in/backs/is ideologically related to could be perceived as the same thing as them accepting the Bitcoins I'd assume so they really need to either return them, which seems difficult, or let them trickle back into the network in such a way that doesn't benefit them or anything that's perceived to be related to them.
So I think the EFF's totally right in doing this. However they probably should've thought of this before they decided to accept Bitcoin donations in the first place.