In YuYu Hakusho, Yusuke's mother was completely written out of the show for some reason...and when I say the show, I mean the show. In the manga, she actually goes with the rest of the characters to the Dark Tournament, but in the show, she's completely absent during this saga, and is never shown reacting to Yusuke being gone for so long.
This is more noticeable because in the very first anime Opening, she's shown alongside the rest of the girls in the stands of the Dark Tournament, but isn't there when the show actually reaches that part.
I'm on Episode 78 right now, and I haven't seen her appear at all or even be brought up since like Episode 20. It's really odd and I can't figure out why they wrote her out---nothing seems to have happened with her seiyuu to have caused it.
Also another anime example that still stings...
No, not the dragon---although he was a casualty of it---but the dude on the left, Misawa, was easily the coolest character in Yu-Gi-Oh GX. Till as of Season 2, they decided to purposefully write him out in a very unsubtle way, with even the characters noticing his lack of presence. In the end, he disappeared for a long time after streaking across campus (one of the reasons I love GX), pops up for a bit in Season 3, and then disappears once more for more or less good.
5D's actually one-upped this, as it literally dumped like six major characters---including the protagonists best friends who he fought to rescue in Season 1---at the beginning of Season 2, and never brought them up again. Really, the whole show had a crazy retool, and apparently it was due to one of the voice actors being involved in a real-life Japanese cult, and thus the show had to be changed and its darker elements removed...but still that doesn't explain why the good guy's friends who were regular folks were booted since they'd easily fit in the lighter retool.