I'm not suggesting that tables be allowed in the SO engine, but I would like to know what pitfalls I can expect if I allow my users to enter them in my (soon-to-be-written) application that allows markup.
If you allow users to enter html markup and you whitelist table elements without providing a proper pattern requirement, it's possible to affect any page's rendering which uses tables as a major layout component in most browsers, sometimes in some very interesting (and/or destructive) ways. Allowing users to generate tables through alternate means is often safer (non html markup run through an engine to create the actual table), if the associated logic pattern for the actual table generation is tight and can't break.
The gist of it is that you can break out of either cells or entire tables within a post (by using unbalanced closing tags), making the content you follow your break out with appear in odd places. This can happen even unintentionally with a malformed table. (unbalanced opening tags can have consequences involving table elements following the content)
I've actually seen this happen before on a major forum (arstechnica.com, back when html was more widely permissible). Unfortunately that was over ten years ago, so I can't link the thread (it involved someone trying to make a table for decibel levels leading up to eardrum rupture, which was fairly amusing when it ruptured the page).
If you're using
divs for all of your layout you're probably fine. If you had strong whitelist pattern requirements for using table elements you would hopefully also be fine.