Any release that omits original soundtrack music because someone was too cheap to pony up a few extra dollars for the rights. Especially when said music is integral to the story, such as WKRP which had most of its music stripped away and when the first season was released people complained so much they've never bothered with any more. Married with Children replaced its "Love and Marriage" theme song with a stupid-sounding instrumental for its DVD release, even though that's the same as taking All in the Family and stripping out "Those Were the Days" and "Remembering You". It's part of the show's atmosphere.
If you include the 1988-89 revival, 9 volumes of the original Mission Impossible were issued to DVD between 2006 and 2012, with the only extras being some episode promos and a holiday message in the very last set, with Paramount Video not bothering to do a single commentary or "making-of" featurette. And when the first several sets were released, Peter Graves was still alive, too.
A&E and the European companies failing to get Patrick McGoohan to record a commentary for The Prisoner.
The first DVD release of the Audrey Hepburn movie Sabrina was awful - grainy picture, for one thing. They later remastered the film for a reissue and it was 100% better.
Any so-called "complete" release of Apocalypse Now/Redux that doesn't also include the Heart of Darkness documentary.
My biggest beef is that when Blu-ray came out for the first year or so it was common to see the DVD version of a movie include all the extras, as well as extended versions, but the Blu-ray would either be a vanilla (no extras) with the theatrical cut, or the extras would be limited to a commentary, or for some inexplicable reason individual extras would be omitted. For example, one of my favorite extras are gag reels and Resident Evil: Apocalypse had a very funny one that still cracks me up. It's on the DVD, but was not included on the Blu-ray, forcing me to keep both (it wasn't issued as a combo pack). The Blu-ray versions of The Fifth Element and Tim Burton's Planet of the Apes omit virtually all of the DVD extras (in the case of Apes, I actually was more interested in the behind-the-scenes stuff than the movie so I've never bothered to buy the Blu-ray).
Fortunately, with the advent of the DVD/BD combo pack I'm running into this less though often the presence of the original DVD extras in the case of reissues is NOT mentioned on the packaging; there have been a few releases I never bothered with initially because I assumed the extras had been cut like with Planet of the Apes, only to find they were there all along - the 2004 Zack Snyder version of Dawn of the Dead comes to mind; I only picked it up because it was on cheap and I was surprised to find the extras - including a related short film featuring Babylon 5's Richard Biggs in his final performance - were included after all.