The only ending I've known to any series (book, movie, TV, whatever) that actually ruined the good things that came before it is Battlestar Galactica. I find it's immensely difficult to actually ruin good things just by following them up with bad things. Even Heroes' first season wasn't ruined by being followed up with complete s*** the entire rest of the show.
Even if you hate Lost's ending, which I very emphatically don't (Across the Sea was stupid, yeah, but meh), I don't understand how that can, for example, possibly invalidate the first three seasons' greatness. They have nothing to do with each other.