Michael Mitzenmacher has an interesting post up comparing citation counts for papers at SODA/STOC/FOCS 2000. The results are quite stunning (and SODA does not fare well). For a better comparison, we'd need more data of course, but this is a reasonable starting point.
As my (minor) contribution to this endeavour, here are the paper titles from 1997-2006 (last 10 years) for STOC, FOCS, and SODA. There might be errors: this was all done using this script. Someone more proficient in Ruby than I might try to hack this neat script written by Mark Reid for stemming and plotting keywords trends in ICML papers; something I've been hoping to do for STOC/FOCS/SODA papers.
If there are any Google researchers reading this, is there some relatively painless way using the Google API to return citation counts from Google Scholar ? In fact, if people were even willing to do blocks of 10 papers each, we might harness the distributed power of the community to get the citation counts ! If you're so inspired, email me stating which block of 10 (by line number, starting from 1) you're planning to do and for which conference. Don't let Michael's effort go in vain !
There are 681 titles from FOCS, 821 from STOC, and 1076 from SODA.