I can't help you too much, I'm affraid, but maybe I can give some pointers that would make it easier on the eyes:

* Allow more HTML input (eg (un)ordered lists are really helpful... <strong>?)
* Get rid of the <table>s, layout can be done with <div>s IMHO
* Giving the messages a fixed width (e.g. 100%) will make it look better in case of small posts
* Make the tread more visible (indenting posts)
* Maybe add a "I've read all of these posts", like Perlmonk's "I've checked all of these".
* "in response to \d+" doesn't say much. I don't remember all the post IDs by heart ;)
* Said before: bright hover colors are too bright (My eyes! Aargghhh!)
* I'm not sure how to make the "index"/"home" page better, but maybe just list threads there?

HTH