Well maybe I am wrong then, but I just watched about 20 different plays from 5 different games just to see and they are in a 4-3 or 4-2-5 (nickel) every time.
http://gamerewind.nfl.com/nflgr/game?id=54972&play=402&icampaign=GR_Free_Clip_nfl*Watched another 20 snaps. It looks to me like they use the 4-2-5 more than anything else. Almost always have 4 down linemen though.
*Watched 20 more snaps. Out of 60 total snaps I saw (3-4) 6 times, (4-2-5) 28 times, (4-3) 22 times, and (4-1-6) 4 times. With Mike Singletary gone I guess none of this matters, but I suspect Aldon Smith will be rushing as a 4-3 DE most of the time whether his hand is in the dirt or not.