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 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. Shredded Moose and Jungle Janet were two others. Clan BOB's Life of Riley was a fairly big long-running comic that disappeared as well.
Life of Riley can be found save for a single missing comic at a mirror site. The community, clanBOB, that formed around it can be found here
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.
Josh Mirman's Stubble ran from 2000 to 2006 with over 700 pages, as the author admits. The author just deleted everything from the site so fan's can't read it anymore, because it wasn't up to his standards. Re-starting the series in 2010, it amassed only 71 pages by the end of 2011 and then halted. Now only two pages are viewable, and the rest is just gone.
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; and the old forum on The Nice is broken. Someone has made their fragmentary archive of strips available here and would love more; contact info available here.
Most of My Cage is MIA although it has started repeating on Go Comics.
The webcomics of Bengo & Pug, Scratchin' Post and Li'l Nyet, disappeared in 2009 when they Rage Quit the Internet over lack of donations. The Li'l Nyet website was reduced to a one-page piece of emotional blackmail, blaming a "mute audience" for their disappearance before the domain lapsed and became a filler page.
The Heroes of Middlecenter went offline some years ago. Because of a "robots.txt" script, the original pages cannot be retrieved by the Internet Archive Wayback Machine.
A Creator Breakdown led John Campbell, the author Pictures For Sad Children, to wipe the website clean. The main comic and his work on various other websites have since been collected for underground distribution. However, the extra Alt Text jokes are likely gone forever, and have been missing since a change of web hosts from back before said Creator Breakdown.
Fireflower, a retelling of Super Mario Bros., vanished from the internet a few months after its conclusion in late 2002. The Wayback Machine only has 3 strips preserved: two random installments from the middle of the story and the farewell strip.