Candidate for worst alternate ending: THE DESCENT. The US version is utterly run-of-the-mill. The UK version (director's cut) is dark, brooding and utterly in keeping with the rest of this terrific film...
28 Days Later has a very bleak alternate ending on the DVD where Cillian Murphy's character dies in the hospital and the others simply walk out of the ward and away down the empty corridoor while the door swings silently shut behind them...
Suggestion for alternate ending: about 2 minutes into Mamma Mia there is an enormous earthquake that shifts tectonic plates miles beneath the island, causing it to be engulfed by the sea, killing the entire cast...