I have been thinking about this for a while. This recently on-hold question really touches my nerve. The question is put on hold due to being too "broad". I will use it as an example to explain my concerns.
First, "broad" (as well as "off-topic" etc) is subjective. In this particular case, I think the question is on the border line at best. I certainly would not vote to close it, even though I am actually quite picky. To most new NGS users, they would think this is a fine question, too.
Second, even if "broad", this question is interesting and useful. It has attracted 4 upvotes in 13 hours, which is relatively fast in this new SE. The answer tells me something new and equally interesting. It has got 5 upvotes, too.
Third, broad questions may inspire epic answers. For this question, someone familiar with QC might take the chance to give a succinct but comprehensive review of existing QC tools and measurements, something you occasionally see at SO or other SE sites. This would be invaluable to everyone. You can't get such an answer from a specific question on a particular technical problem with a QC tool.
Fourth, at this particular time we are struggling to pass the private beta phase, I speculate that closed questions are not counted. @RobertCartaino said we had less than 75 questions a couple of days ago. However, as @gringer pointed out, we had 77 questions almost at the same time. In addition, on the question page, we have 102 questions right now, but on the Area51 page, we only have (15+1)*4.9=78.4 questions. Why the difference?
Finally, even if not just for private beta, we need both experts AND new users to keep this site alive. To me, the questions here are a little too "narrow". They focus too much on specific technical issues. Questions slightly deviating from this focus quickly got downvoted or closed. Note that we are competing with BioStar. Although criticized for all the problems, its broadness and friendliness to newcomers are undeniable. If we keep closing border-line questions so aggressively, we would push new users to biostar and finally kill this SE, again.
So, please refrain from closing proper but imperfect questions so quickly.
EDIT: here is a list of questions that are currently closed or put on hold.
Influential papers. I wouldn't vote to close it, but I can understand why others want.
Bioinformatics vs biostatistics vs computational biology. Hmm... same comment as above.
Stable download URL. A little general, but I think it touches a real problem. I have voted to reopen it.
QC for NGS. This is the question I was mentioning at the beginning. It is a proper question.
Smalt. This is a good bioinformatics question and should not get closed.
Public multi-omics dataset. This is a good and relevant question. Many newcomers will have the same question. The answer has got 6 upvotes.
Constructing gene network. I am not familiar with the topic enough to tell.
NGS metadata schema. OP was essentially asking what relationships are common to general schemas. This is a proper question and should not be closed. Even if there were no general solutions, this would not make the question itself non-specific.
Scripting parallel processing. Closed due to off-topic. I don't think it is bad enough to merit a closure. @DevonRyan's answer is informative. Note that OP is a highly experienced SO user. He/she did not show up after this question.
On bootstrapping. Closed due to off-topic. OP has really put a lot of efforts into the question. The answers are good, too. I don't think it is that off-topic, either. We use bootstrapping often. Again, we pushed a potential new user away.
Genome vs transcriptome. Closed due to off-topic. New bioinformatics students with a CS background are likely to have the same question. I don't see we should close it. Again, OP was asking only one question and then gone.
Difference between common formats. Closed due to too general. I don't see the point: a basic question may look general to experts, but it is often a good one to many people. The answers are very helpful.