My own forum was completely swamped with SEO spam and I constantly get several new spammers signed up every day, just because punBB is known to be allowing SEO spam like this. Fixing it is very easy though and I have just corrected it on my own forum.
Assuming you have version 1.3.5, just follow these steps:
1. Open the file include/parser.php
2. Find line number 609, which will look like this: return '<a href="'.$full_url.'">'.$link.'</a>';
3. Change it to: return '<a href="'.$full_url.'" rel="nofollow">'.$link.'</a>';
4. Save and upload your modified script.
This will add rel="nofollow" to URLs in posts and signatures. You may need to reapply it when you update though. If you have an earlier version, you should either update or you will just have to find where the line is located in your version yourself. It belongs to the handle_url_tag function.
A plea to the development team: please add this permantly! 