No, but we could start one. Maybe even with this thread.
I would suggest that people post what they know and you merge their findings into your initial post listing the changes by year. Posting wrong information usually gets quicker answers to straighten things out than posting the correct information for some reason.
1997 was the last year with the old, good looking, Cagiva font on the tank. It said Ducati in big letters, silver with gold edges, and Monster underneath in black (red on the black ones). It was the first year of the M750 in the USA, which was only available in silver that year.
1998 was the first year of plastic side panels instead of the nicer looking carbon fiber. The tank only said Ducati on it, in the same font they use today, which has less character.
1994-96 had no cowl on the bars, although apparently a few 96 models came with them. The cowl was standard on the 1997 M900.
1994 and 1995 had a choke knob up near the triple clamp somewhere. 1996 and onward had a bar mounted choke rotating around the handlebar and activated with the left thumb.
1997 had small valve heads on the M900, which was apparently the only year they did that. It have more midrange power, but less top end.
2000 was the first year of a fuel injected engine for the M900.
Well to try and hit stuff that hasn't been hit:
'03 Models changed to 620, 800, and 1000. 620 5 speed, wet clutch; 800 6 speed, wet clutch; 1000 6 speed, dry clutch
'04 S4R introduced
'04 620 is given a 6 speed and a slipper clutch