Do you know any of the instruments they played? Or what style of folk? (ie, Irish, Celtic, American, pop folk, etc?)

Also related to the search, it appears as if the club only ran from about 1980-April 1991, so if it was in the 90s as you recall that greatly helps narrow the search window.

Currently the two best matches I've found:

First is a group called "2/3s Home" comprised of Jonathon Bachelor, Kuntari Bachelor, and David Paul, who performed there in Jan 1988 (click for more)

Second is Marcia Bowman, Tom Cahoon, and Charlie Holdaway, who played at least thrice (May 1986, July 1986 and January 1987). This one's particularly promising to me because you can hear a sound bite (click) and because Tom's website is up and running with the following blurb:

“The Grass Is Always Greener"
These songs were originally recorded in 1986 and released on cassette. At the time, I was playing in a folk music trio. There were only a handful of coffeehouses in San Diego where acoustic music, and particularly original songs, could be performed. Over the years, many people told me how much they still enjoyed listening to the tape, so I had it re-mastered for CD. (link)

I also found the following groups which were identified as trios:
- Backsreets (bass, banjo, and guitar; members not identified) September 1982 and August 1983
- Charter Flight Trio (instruments and members not identified) March 1983
- Gypsy Moon Trio (original songs and "international folk music"; Paul and Carla Roberts and "Fiddlin'" Floyd Fronius) May 1983, August 1983, November 1984, January 1985, February 1985, March 1985
- The Swingtime Trio (blues, folk and traditional music; members not identified) November 1984
- The Epicenter String Band (hammered dulcimer, fiddle, guitar; performers not identified) June 1985, February 1986
(This list is NOT complete and is just a listing of bands I saw when I put ["Drowsy Maggie's" trio folk] in California into newspapers.com)

Are these ringing any bells?