Is there a reason that all links are now treated with rel="nofollow"?
This wasn't originally the case.

This is to discourage signature link spamming and similar "SEO" tricks. I think it's been in use from the beginning of the current forum software in 2006.

No it wasn't always so. It's only within the last year.

What about legitimate signature links?

No, it has been that way if not from the beginning so for a long time.

As much as I hate to disagree with you, I used to have links reported from this site to mine in Google's webmaster tools.

They have disappeared within the last year.

Maybe a glitch. Nofollow is meant to be there anyway.

Signature links work just fine, and other forum users can use them to find out more about you.

But as the others indicated, we configured this forum software to use rel="nofollow" on all user-provided links (including signature links) a long time ago.

It's possible that we initially configured it to use rel="nofollow" on message links but not signature links, and then later configured it to use rel="nofollow" on both message links and signature links. But if so, we made the change a long time ago.