I'll stick to international/national/tour shows, since I think we've all been to some pretty empty local shows. Some of the shows I list did have a good amount of people (like 50-100), but they were shows booked in large-size venues so it looked really empty by proportion. I also included shows where I think the band should have had drawing power well over what they actually brought out.
EDIT heh, I'm the only one who's made a big list so far, but while the first show answers the topic, I'll leave the rest there for your perusal.
The Gates of Slumber in August 2007 - about a dozen people there. Gates put on an incredible set and made me a new fan. Most of the others already knew them; I think I may have been the only person to come to the show as a total stranger.
Kayo Dot in Detroit in October 2005 - they started out playing to maybe 25 people who were just there hanging out, of course by the time the first song was over the place had cleared! haha. About 7 or so people stuck it out.
Dark Tranquillity in March 2006 - this was a side-show they'd booked on an off-date during the Opeth/Devin tour. Maybe 2-3 dozen people showed, but they were all into it, which was really cool. Mikael Stanne remarked during the show that we were the smallest crowd they'd ever played to.
Symphony X in May 2003 - dismally attended show that resulted in Harpos cutting their set short due to nobody being there. Shame.
Lacuna Coil in November 2003 - there were probably close to 100 people here, but it was in a huge venue so the place looked dead.
Moonspell played to a dead house in October 2006 after all the Katatonia fanatics dispersed during that tour.
Therion in 2005 - awful. Attendance was so low I felt kind of embarrassed for Christopher & the band.
Satyricon in 2004 - maybe 75 people in a huge venue that looked disproportionately vacant. The band put on a fantastic show. On this tour they played the day after a Cradle of Filth show at the same venue - I think we can guess which show most of the kiddies picked.
Morbid Angel in 2005 - 50 people at best; David Vincent remarked "I'd like to thank the few people who are here, for braving it to come see us" (the weather was really bad that day)
Kamelot in 2006 - probably over a hundred people, but again in a big house.