Why are so many sites in Area 51 still on public beta, even if they have completed the beta phase?
See this blog post, in which Robert explains that even after the initial 90 days sites won't graduate until they have enough high rep users, so that the site can still work with the non-beta reputation requirements. Basically that means that a site needs an excellent score in the "avid users" category.
A site won't graduate until Jin has finished its design. Since Jin can only do so much work at a time, there is currently a queue of sites which meet the graduation requirements, through which Jin is working one by one.
See also this excellent answer by Michael Mrozek on the Unix & Linux meta site.