Yeah, in the animated series of Spider-Man, GG threw MJ into a portal and she disappeared. She returned later on in the series without so much as an explanation, but then I guess, what else is a portal good for, other than safe-keeping?!
I don't really care much for Spider-Man continuity, even in the comics these days - it's been FUBAR'd since well before the movies. Gwen wasn't the only love interest they merged into the character of MJ - after all, it was his first love (or maybe I should say 'crush', as they never got together) Liz Allan who ended up marrying Harry Osborn. This is no big deal for me, as Liz Allan was a pretty nothing character in the grand scheme of things.
And Darth Simon, what the heck are you talking about? Hobgoblin was introduced WAAAY later in the comics than Green Goblin...in fact, I read the issue that introduced the Hobgoblin nought but a few days ago - GG and Doc Ock were mentioned in the past tense within the first few panels. Funny thing is, the same issue introduces MJ as well!