The original form of Strip #43 has only been mentioned in the author's (Scott Ruhl) comments. Even the webmaster of the site has never seen it - although considering the pun involved with the final strip, one can imagine why Scott Ruhl withheld it from publication.
A lot of the original Magiversity strips were lost when The Duck crashed in 2005, as the creator didn't have backups.
This◊ Penny Arcade comic was taken down after a cease-and-desist from American Greetings.
There were three strips that were made exclusively for members of Club PA (a club for everyone who donated to penny-arcade.com in the early 2000s), which were never released to the public. One involved Gabe and Tycho discussing Club PA and its members. Another was an animated strip of Tycho sitting on the couch, looking around and sticking his tongue out, with a caption reading "Tycho might be crazy." The third strip was a sketch of Pac-Man shooting Gabe in the leg. These strips have been posted on the Penny Arcade forums, and they can be viewed here◊, here◊, and here◊.
Most of David Willis's "proto-Shortpacked!" strips have been completely removed from his sites. A few were later on brought back when some filler was needed, but the majority are gone. They've since popped up in the first book collection—which then proceeded to spend a good two years or so out-of-print.
The website for Platypus Comix is missing several stories from Mulberry, Keiki, Scrambled Eggs, and the Variety Section. Most of them have apparently become Old Shames for creator Peter Paltridge. Examples that should stick out to people who don't read the list he wrote of all the comics he posted on the website include the first Mulberry comic, the second Keiki storynote Actually, the part where the archive skips from 1 to 3 skips over more than one story, and half of "Raiders of the Lost Arc" (one of the comics found in the Variety Section). Sometimes, he publishes books containing comics he deleted from the website.
The Internet era has created a new type of Missing Episode. Increasingly, promotional web-only tie-in stories or games are used on official sites to promote a product, event, or work. Once the promotion has run its course, the official sites may disappear, along with all that tie-in material. And the relative complexity of a web-hosted multimedia work makes it difficult to just Keep Circulating the Tapes. To take just one illustrative example, comics writer Gail Simone wrote a Superman interactive webcomic story for an official Pepsi Superman Returns promotion. Since the Pepsi promotion ended long ago, and its site is now defunct, if you didn't read it at the time, odds are you never will.
As mostly amateur projects, webomics are heavily prone to this. Many cease updating when the creator loses interest or has no time to continue drawing. When the host shuts down or the creator doesn't renew their account, the website disappears and takes all the comics with it unless die-hard fans took the opportunity to archive everything.
The rerunning of Roomies!, It's Walky!, Joyce and Walky! at BringBackRoomies.com is dead-set on averting this, turning up everything from out-of-print print-only material to stuff that never made it to the public to begin with. Especially notable is the print-exclusive from the third issue of Keenspot's Roomies! comic book, which Willis accidentally neglected to put in any of the official collections and thus spent almost a decade completely unavailable.
While many of The Parking Lot Is Full's strips are now on a memorial archive site, many others are currently missing from the internet.
A lot of David Gonterman's old work from the days he was a big Sonic the Hedgehog and Sailor Moon fan are missing, though mostly his web comics. Among those are is the last issue of "Sonic: The Mobius Chronicles" and most of "Sailor Moon USA". His fanfics, on the other hand, are a different story.
Almost the entirety of the original Shredded Moose. This is because of Old Shame of the two creators and the fact it could harm the career of the artist.