I have an idea on how to implement static url's to please search engines. I'm no expert on rewrite rules, so please bear this in mind when you red my idea.

I would like the table of posts to change link to this format
/thread/550
insted of the default
/index.php?mode=thread&id=550

The pages which links to posts should be
/page/2
instead of
/index.php?mode=index&page=2

This way all threads would have one link, and one link only, from the front page. You can login to Google Webmaster Tools and tell it to exclude parameters. I believe this would please Google and hopefully index your content much better.

Now I have a problem since
/index.php?mode=thread&id=550
is the same as
/index.php?id=550 (I've modified it a bit)
which is also the same as
/?id=550