There are so many of these I've still not played, I can't really be comprehensive.
In terms of best, Stargate on the DMD side for me. Alpha-numeric Hoops I feel has the best rules. Silver Slugger is the most flow layout from the era I've played, and I enjoy that one.
Worst ones for me were Barb Wire (the one I played was purportedly restored but felt practically unplayable, so this may be more the specific game than the design) and Super Mario Bros. I found pretty dull (however, I did think Super Mario Bros. Mushroom World was an entertaining little game).
My overall assessment of System 3 likely mirrors many others. Great deal of layout experimentation (not EM era levels but more than the other SS manufacturers were doing), but compromised by generally poor rule design (competitive rule balance was not a priority of Premier) and of course the unpopular flipper mechs.