Misfile is a bad manga imitator (plenty of manga with far stronger storylines if this is what you want) and Menage a Trois is smut filth drawn by someone who has never gotten laid or who, despite having been laid, still has nothing but seventh grade ideas about sexuality and humor involving sexuality. Megatokyo has a plot like you can get used to being raped in prison.
Sluggy had good storylines even through the pirate mess, but this latest 2 year Riff stint just seemed to drag on and on and on without ever going anywhere. I feel like if this was the type of strip they want, they need like 12 panels a day to keep crap moving at anything resembling a reasonable rate. Obviously that is demanding, but this storyline even finally kind of killed my enjoyment of the strip, and they had as much of my goodwill as any strip could have (used to be my favorite).
Evil Inc., Girl's Genius, Irregular Webcomic, and Order of the Stick have pretty good contiguous plots. For dead webcomics, Bruno the Bandit, Gaming Guardians, Grim Tales from Down Below / PowerPuff Girls (both from snafu-comics, pretty much the only good fanfiction ever), Marry Me, Patchwork Champions, and Wigu I remember as having strong plots depending on the particular type of plot you value, e.g. gaming, adventure, snark, et cetera. I am sure I am forgetting more dead ones, there are tons of good comics that finished instead of dragging on forever.