On the STOC graph, the bold locations indicate years when STOC was held at FCRC. After a relative decline in the late 1990s, the number of STOC rose steeply from 1999 to its current peak in 2002. Surprisingly, STOC 2004 accepted the fewest papers in ten years, despite having the second-highest number of submissions ever. The record-low acceptance rate didn't seem to hurt submissions in 2005, though.
The FOCS graph does not include this year's results; I'll update the graph as soon as the information becomes public. Thanks to Sariel for this year's numbers! Since its low point in 1996, the number of FOCS submissions has been rising steadily, except for a temporary dip in 2000 and 2001 and a spike in 2002. Again, FOCS 2003 accepted the fewest papers in ten years, despite having the second-highest number of submissions since 1990. The record-low acceptance rate didn't seem to hurt 2004 submissions, though. Update (June 22): Once again, despite a near-record number of submissions, the FOCS PC chose to accept a near-record-low number of papers, apparently because parallel sessions are evil. Evil! EEEEVVIIILLLL!
Despite a significant rise in the number of submissions, the number of acccepted papers has been almost constant at both STOC and FOCS since the late 90s, with two exceptions: a temprorary rise in 2002 (in response to submission spikes) and a temporary dip in 2003-04 (in response to the SARS epidemic, or the beginning of the Iraq war, or the release of The Matrix Reloaded, or something)
Based on this data, the STOC/FOCS theory community appears to have had a growth spurt in the early 00s, but it is unclear whether the community is still growing or merely holding steady.