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I'm looking to do some research into how RSA is used in the wild. I've read through a few papers and it seems other researchers have had no trouble collecting millions of keys to perform analysis on.

I've done some preliminary research but can't seem to find any one site from which to download other people's public keys.

I assume that given the nature of public keys that it would not be a privacy risk to have this sort of database available to the public.

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You probably could extract a bunch from the public SSL Observatory data dump. –  CodesInChaos Mar 10 at 14:37
Query the top sites from the Alexa rankings and read off the SSL transcript? –  figlesquidge Mar 26 at 13:20

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