If I am right, at StackExchange, a new or newly edited question and a question with a new answer will always be placed on the top. On the other hand, the new BioStar has a ranking system, which seems to prefer popular questions, though admittedly I do not know how exactly it works.
Personally I much prefer the StackExchange way. For a Q&A site, the key feature is to get a question quickly answered and to update its users with latest answers. In the BioStar ranking system, if a specific/hard question cannot attract attention in a few days, it is likely to be buried forever.
For example, I answered a question on the difference between samtools and gatk asked 4 days before my answer. After I answered it, the topic was on the 3rd page. Except the OP and a couple of others involved in that thread, few were aware of the new answer. I know it was on the top of the "Recent" page, but personally I rarely click that tab and on that tab, my answer would be quickly pushed to 2nd page by comments. Note that I am not saying that my answer is anything good. I just think in the angle of both a questioner and answerer, this behavior is a little frustrating.
In my view, we should revert to the StackExchange-style question ordering. It is more appropriate for a Q&A site.
(As a side note, I found StackExchange's search was more accurate. This could be just my illusion and I couldn't access the old site any more to confirm this. Also, the StackExchange's similar/related question sidebar was quite useful. I wonder if we could implement something similar or just grab their code.)
EDIT: Interestingly, when I log in, the questions are sorted by creation time by default; when I don't, the questions are sorted by "rank" and my this post is placed at the 8th place in this ordering. I forgot how the questions were sorted when I checked that samtools-gatk question. But anyway, I prefer the StackExchange ordering. Furthermore, the views/votes/answers ordering discourages small subfields and recent questions. "Sort by edit" is also a little confusing. I am inclined to removing them.
EDIT2: Edit to see if this puts the post on the top. -- Yes, it is, the SE behavior.