BobS is most definitely up there. Who was that other guy who saw them an unbelievable amount of times? Was it Franz or something like that?
Not sure how many times Franz has seen them, but I'm sure it's plenty. I think you're probably referring to a German guy by the name of Matthias who had seen them like 50 times by December of 1998 (MP mentioned this on the bootleg of one of the shows). However, I remember asking MP about Matthias several years ago, and he was under the impression (altho not confirmed) that Matthias may no longer be with us.
Anyhoo, time for me to update my personal list:
06/29/93 - Milwaukee, WI (Summerfest)
11/04/94 - Milwaukee, WI
11/03/97 - Milwaukee, WI
11/18/97 - Madison, WI
05/13/98 - Chicago, IL
02/02/00 - Santa Ana, CA
02/04/00 - Los Angeles, CA (infamous Firemarshall show)
02/05/00 - Los Angeles, CA
08/18/00 - San Diego, CA
08/20/00 - Los Angeles, CA
08/21/00 - Los Angeles, CA
03/07/02 - Phoenix, AZ
03/08/02 - Los Angeles, CA (first performance of 6 Degrees title track)
03/15/02 - Chicago, IL
03/16/02 - Chicago, IL (Master of Puppets show)
03/17/02 - Milwaukee, WI
08/09/02 - San Diego, CA
08/10/02 - Los Angeles, CA (first performance of Instrumedley)
07/11/03 - Wantagh, NY (performance of The Necromancer)
08/02/03 - Seattle, WA
03/06/04 - Los Angeles, CA (WDaDR show)
03/07/04 - San Diego, CA
03/08/04 - Phoenix, AZ
03/30/04 - Wallingford, CT
04/01/04 - Boston, MA
04/02/04 - Philadelphia, PA (performance of Echoes pt. 1)
04/03/04 - New York City, NY (first performance of Disappear, and guest appearance of Eugene Friesen)
09/05/04 - Madison, WI
09/19/04 - Los Angeles, CA
07/24/05 - Los Angeles, CA
07/28/05 - San Diego, CA
03/09/06 - Anaheim, CA
03/10/06 - Los Angeles, CA (performance of Sheep)
03/28/06 - Philadelphia, PA
03/29/06 - Wallingford, CT (recorded for In Constant Motion DVD)
03/30/06 - Boston, MA
04/01/06 - New York City, NY (Score show)
07/24/07 - San Diego, CA (first performances of ItPoE, Schmedley Wilcox)
07/27/07 - Los Angeles, CA
08/20/07 - Buffalo, NY
08/21/07 - Boston, MA
08/22/07 - Wallingford, CT
08/24/07 - Holmdel, NJ
08/25/07 - Wantagh, NY
08/26/07 - Philadelphia, PA
05/02/08 - Los Angeles, CA (first ProgNation date)
08/29/09 - Los Angeles, CA (featuring DrumNation 2009 and an extended jam with Dweezil Zappa and Steve Vai)
09/25/11 - Los Angeles, CA (first performances of Far From Heaven and Breaking All Illusions)
12/01/11 - San Diego, CA
12/02/11 - Anaheim, CA
07/02/12 - Los Angeles, CA
07/03/12 - Anaheim, CA
04/06/14 - Milwaukee, WI
05/06/16 - Los Angeles, CA
Side Projects/DT-related bands01/30/99 - Los Angeles, CA - LTE
02/01/99 - Hollywood, CA - LTE
05/05/99 - Hollywood, CA - Planet X
09/01/00 - La Mirada, CA - TA
01/20/01 - Anaheim, CA - TA
06/27/01 - Anaheim, CA - G3
06/28/01 - San Diego, CA - G3
06/29/01 - Los Angeles, CA - G3 (with Paul Gilbert & Steve Lukather for jam)
11/23/03 - Whittier, CA - Neal Morse
09/18/05 - Chicago, IL - CatSM
05/27/06 - Whittier, CA - AJ
03/18/07 - Los Angeles, CA - G3
03/19/07 - Anaheim, CA - G3
06/27/08 - Downey, CA - LTE
04/17/10 - Downey, CA - TA
02/25/11 - Long Beach, CA - YMC
09/02/11 - Santa Ana, CA - AM
01/14/12 - Los Angeles, CA - PSMS
01/20/12 - Anaheim, CA - PSMS
09/04/12 - Anaheim, CA - FC
03/26/14 - New York City, NY - TWD