Bracketing out the randomness of the universe and the effect of events on the political landscape, I don't fear Guiliani in the general election. Given his troubles in the primary, he won't generate any fervor with the republican base, whose evangelical component--to grab one example out of the air--seems to be showing signs of disillusionment/fatigue with their adventures in politics, regardless of the ideology of the republican candidate.
Hillary and Obama, except in terms of rhetoric on the war, haven't made any sort of committed leftward swing, so should be ably to nimbly make the classic push toward the center in the general election. And then it seems to me that Guiliani's centrism, which he'll have to emphasize to court persuadables, will make the democratic candidate more palatable in the eyes of republicans and independants. It's not that an immoderate republican would actually vote for a dem, but that they'd be much less motivated to vote against one. Sort of like all those moron democrats who saw little difference between Gore and Bush.
More important than the above considerations, though, I would say that Rudy's primary campaign slide has less to do with his ideology and a lot to do with what people are learning about both who he is and his track record. A candidate's nature is obscured in the general election by the white noise of so many media representations, but Rudy's gaffes and his checkered past seem to me to have a flavor that punches through that veil. The rhythm of his speech is part of this. W, based on some sort of primitive instinct I think, is much cagier about not ever letting a real emotion come out. Guiliani, on the other hand, seems much more prone to feeling justified in his borishness in a way that a) he can't control and b) is personal in a way that transcends ideology.
Compared to a campaigner as blandly conservative (in approach) as Hillary Clinton, I think it would be difficult for Rudy not to come off as an erratic and generally disagreeable figure.