I've been using kdiff3 even though it hasn't been updated in a very long time because it has one killer feature: manual diff alignment. I can select a token in both (or all three) files and then force the diff to align at that point. It makes merges a whole lot easier. Sometimes, a single realign is all that's needed for a file merge to sort itself out. Even when that's not the case, it's easier to reason about the changes.
Did I miss something? That is, is that feature available in other diff/merge tools and I just haven't seen it?