Kid Radd, a cult favorite among those who have been on the Internet a while, originally got screwed by the Internet with newer releases of IE and Firefox making the comic obsolete (the site was meant to work with IE5 and the original Firefox). Dan Miller, the author, did have multiple methods of viewing the comic — either on downloadable archives or sites where you could find the older versions of IE and Firefox that work perfectly. Unfortunately, AT&T recently shut down its WorldNet Web hosting server, taking all of Dan Miller's wondrous comic with it. Luckily, a fan has saved the online version on his own site, but the fanbase was sweating for a while there.
Any webcomic that's gone offline, for that matter. Jungle Janet and Shredded Moose were two others. Clan BOB's Life of Riley was a fairly big long-running comic that disappeared as well.
This is what happened to the webcomics hosted by online comics syndicator Full Tilt Features. Notably Lamtoon by Matthew Meskel, which was syndicated via RSS to LiveJournal at the height of its popularity. It went offline when Full Tilt Features went offline, and Meskel never continued the strip afterwards, so Lamtoon comics are now EXTREMELY rare (but still out there).
Josh Lesnick's Wendy, the predecessor to Cute Wendy and eventually Girly, has being disavowed by the author and it is impossible to find it online.
Two comics, Land of Lost Mythology and Coma Dreams by the same author (Kasey aka Maelstrom) were known for an intricate and detailed art style reminiscent of Maurice Sendak, with compelling storylines and characters. Both comics ended in the middle of their story arcs, with no indication what happened to the author, or why work on the comics was dropped. An archive for Coma Dreams still exists, but Land of Lost Mythology is no longer available anywhere online and the author has been unreachable since 2002; although the old forum on The Nice is still accessible.
Most of My Cage is MIA although it has started repeating on Go Comics.
Not in My Backyard!, a very early webcomic (as in, 1998 early) stopped abruptly in 2001. The site was still up until 2011. Fortunately, Wayback has saved it.
