Space Mountain would go on my list. Splash is my favorite ride anywhere and the only attraction at Disneyland that we will plan a trip around. First question when planning a trip: Is Splash open. Love Big Thunder at night so it stays too.
I like 'em all, and they all have a history; either by way of age and class (Thunder), Walt's vision (Space), or Disney animated classic (Splash).
If I had to choose I guess it would be Thunder. Both Splash and Space have an exhilarating edge to them. Thunder is a super attraction and has great theme to it as well. But I could see something like the Mine Train coming back in its place, as someone else noted here. A place to showcase more audio-animatronic figures in an area that is heavily themed to the frontier. Seeing that train traveling along the river again would be cool. And there's definitely enough room for another slow-moving themed attraction. Not everything has to be a white knuckler.