Anonymity was encouraged, which was great - it made absolutely no difference what one looked like, what gender they were etc.
There was no specific focus on making friends. In my opinion, joining something that has a friend-making purpose immediately makes it a bit awkward and makes interactions somewhat forced. Much better if friendships are forged 'accidentally', which happened a lot on those websites.
Threads and replies would be sorted by latest post, not by any notion of 'rating', and threads would never really expire. These made conversation more natural and discouraged people from just posting what they thought would be popular or risk not being even noticed.
After a while, people might have exchanged instant messenger contacts, which also had the benefit of being anonymous. People also were not online all the time, so could 'disconnect' any time, which also helped with feeling comfortable about it.
Search engines would show these message boards in search results, which meant that like-minded people would find them in similar ways and already have something in common.
Then antisocial media came along and made us all less connected.