My alltime favorite, the mass usage of subdomains... Search engines are the largest incoming referrals of users (at most large communities anyway); utilizing subdomains is like using a seperate domain for your sections; which will highly impact your search engine rankings.
A site at http://www.undergroundnews.com
is NOT the same as a site on http://www.undergroundnews.net
, they are seperate domains, additionally using a subdomain for content like forums.undergroundnews.com would be the same as using a seperate domain in accordance with search engines.
So, if you have an active forum with a ton of content for spiders to eat up, whichever domain the forum is hosted on will be accredited with the se bonus as the forum is hosted on that domain.
This means if you have say 200k links to your forum, and 50k links to your site, it'll vary what your SE ranking is depending on the domain used (may it be http://www.mysite.com
Broken down with the data from my example with the usage of subdomains: http://www.mysite.com
Broken down with the data from my example without using subdomains: http://www.mysite.com
250k (with both sets of data combined).
A lot of sites utilize subdomains for organization, however they are unwittingly cheating themselves out of valuable rankings to their site.