Hmm, a good question, and one I don’t have the answer too unfortunately.
I have used Vbulletin before, which I still consider to be the number one in forum software, but as mentioned above, this certainly has its drawbacks. The messy table code being one, but I think the most vital one is the ease of templating, it is very difficult having to use the admin styling system apposed to the simple stylesheet you can edit in your favourite editor.
I have also used IPB, and PHPBB again both have drawbacks.
I have recently started using bbpress which accompanies WordPress, and this seems much nicer to code for, but I am still in the early stages of that so can’t fully decide where this one lines up.
Would like to know what everyone else thinks the best forum software is.