user107: My question was flagged for closing for, in part, not having a definitive answer. While there may not be a single definitive answer, there certainly can be a best answer of multiple possible correct answers.
How do we wish to handle questions like this? I have seen many many similar questions on other SO sites.
We have:

What conditions should I use for Gel Red staining?
What are the main mechanisms of interaction between the nervous and immune systems?
What are limiting factors for intron length?

So I think we are going to run into lots of these.

user25: The degree of subjectivity in your "good resources" question is far higher than any of the other three.  Answers to the others would generally be supported by more facts and less opinion.  Sure, there's a degree of subjectivity in virtually all questions, but yours is something of a double-whammy between being a list, and a list about learning methods.
I'm more laissez-faire for the moment with some other "resource" questions like this:

Good source that explains the evolution of single-celled organisms "from scratch"

as it's far less subjective.  I am not out to close all questions with hints of subjectivity, but yours is far beyond the pale.

user6: There doesn't need to be one single correct answer for a question to be allowed here. What is problematic in the Q&A system is questions with a large number of equally valid answers. 
One problem with recommendation questions is that voting doesn't really work anymore, the votes are not based on the quality of the answer anymore, but purely on the popularity of the recommended item. 
The other big problem with broad recommendation questions is that they tend to get a lot of answers. Questions with a lot of answers are very problematic and need a lot of maintenance. SE even implements a maximum number of answers for that reason, if you reach that limit no more answers can be posted. One big problem is that nobody reads all these answers anymore, users just add their recommendation without checking if it is already there, leading to duplicate entries. 
But there are recommendation questions that can work well on SE sites, the defining characteristics of those are that they have objective criteria to evaluate the answers and that they have a reasonably limited number of possible answers. The more specific the question is the better it works usally.
Now, to the questions you mention, the latter two of those have a limited amount of valid answers. They are not at all subjective, you can evaluate the answers on purely objective terms. 
The first one sounds at first like a protocol recommendation, which I would consider valid as long as there are some criteria in the question on which the answers can be evaluated. "What's your favorite protocol for [X]" type questions are not something I'd like to see here. But this specific question is also more of a troubleshooting question, the title is somewhat misleading here and it might benefit from being edited into a question more of the form "I have problem [X], how can I solve that" and making the protocol secondary.
Now, your question is a recommendation question. The problem I see with this one is that it is very broad and provides not enough criteria by which we could evaluate the answers. Being able to understand Nature, Science and Cell is unfortunately not a helpful criterion, those journals cover a very large part of the natural sciences, not even only biology. I can imagine a very, very large number of possible answers to your question, most of them equally valid. 
Now, the question is partially redeemed by the good first answer, that doesn't just dump one recommendation but gives some more detailed advice. The other answers are typical of what you usually find in this kind of question, 1-2 links to possible resources with minimal amount of detail provided. One is even a recommendation for a book the answerer hasn't even read yet.
I'm not completely against recommendation questions, but they should provide a lot of detail and be as specific as possible. This one is just very broad, and questions like this are especially problematic in the early beta. They will be used as an argument to ask similar questions. I probably wouldn't mind this question all that much if it had occured 90 days from now, but for now I think it should remain closed. 

user57: As the responsible party for What are the main mechanisms of interaction between the nervous and immune systems?, I wanted to offer that it differs significantly from a "list" type question.
From the resource yamad cites (I'll grab a few points that are applicable):  

Great subjective questions insist that opinion be backed up with facts and references

It is an active area of research, and can be backed up by scholarly references.  It is slightly open ended, as someone could say "it occurs in X system" and someone else "in Y organ" (I'm being over-simplistic, I realize).

Great subjective questions have a constructive, fair, and impartial tone

I'm not asking what people believe to be the best or their favorite interactions between the two systems, I'm (implicitly) asking what the scientific consensus on the matter is.  With a site like this one, that has to be an assumption that underlies all questions, or else most would be "bad" subjective and have no definitive answer.

user72: I think SE sites are ideal for collecting shared wisdom about quality resources. Questions like https://stackoverflow.com/questions/562303 are among the most useful questions on SO for me. Where else can a person get the benefit of a set of experts vetting the best resources to learn from?
My take on perusing SO is that "what's the best"-style questions are closed for being subjective. However, "what are some resources"-style questions are generally not closed. I'm not sure I can put the distinction into words, but I would vote for drawing a similar line.
Then there is also the word from on high: Good subjective, bad subjective from the SO Blog

107: <p><a href="https://biology.stackexchange.com/questions/122/what-are-good-resources-for-self-learning-modern-molecular-biology-concepts">My question</a> was flagged for closing for, in part, not having a definitive answer. While there may not be a single definitive answer, there certainly can be a best answer of multiple possible correct answers.</p>

<p>How do we wish to handle questions like this? I have seen many many similar questions on other SO sites.</p>

<p>We have:</p>

<ul>
<li><a href="https://biology.stackexchange.com/questions/101/what-conditions-should-i-use-for-gel-red-staining">What conditions should I use for Gel Red staining?</a></li>
<li><a href="https://biology.stackexchange.com/questions/27/what-are-the-main-mechanisms-of-interaction-between-the-nervous-and-immune-syste">What are the main mechanisms of interaction between the nervous and immune systems?</a></li>
<li><a href="https://biology.stackexchange.com/questions/72/what-are-limiting-factors-for-intron-length">What are limiting factors for intron length?</a></li>
</ul>

<p>So I think we are going to run into lots of these.</p>
 25: <p>The degree of subjectivity in your "good resources" question is <em>far higher</em> than any of the other three.  Answers to the others would generally be supported by more facts and less opinion.  Sure, there's a degree of subjectivity in virtually all questions, but yours is something of a double-whammy between being a list, and a list about learning methods.</p>

<p>I'm more <em>laissez-faire</em> for the moment with some other "resource" questions like this:</p>

<ul>
<li><a href="https://biology.stackexchange.com/questions/115">Good source that explains the evolution of single-celled organisms &quot;from scratch&quot;</a></li>
</ul>

<p>as it's far less subjective.  I am not out to close all questions with hints of subjectivity, but yours is far beyond the pale.</p>
 6: <p>There doesn't need to be one single correct answer for a question to be allowed here. What is problematic in the Q&amp;A system is questions with a large number of equally valid answers. </p>

<p>One problem with recommendation questions is that voting doesn't really work anymore, the votes are not based on the quality of the answer anymore, but purely on the popularity of the recommended item. </p>

<p>The other big problem with broad recommendation questions is that they tend to get a lot of answers. Questions with a lot of answers are very problematic and need a lot of maintenance. SE even implements a maximum number of answers for that reason, if you reach that limit no more answers can be posted. One big problem is that nobody reads all these answers anymore, users just add their recommendation without checking if it is already there, leading to duplicate entries. </p>

<p>But there are recommendation questions that can work well on SE sites, the defining characteristics of those are that they have objective criteria to evaluate the answers and that they have a reasonably limited number of possible answers. The more specific the question is the better it works usally.</p>

<p>Now, to the questions you mention, the latter two of those have a limited amount of valid answers. They are not at all subjective, you can evaluate the answers on purely objective terms. </p>

<p>The first one sounds at first like a protocol recommendation, which I would consider valid as long as there are some criteria in the question on which the answers can be evaluated. "What's your favorite protocol for [X]" type questions are not something I'd like to see here. But this specific question is also more of a troubleshooting question, the title is somewhat misleading here and it might benefit from being edited into a question more of the form "I have problem [X], how can I solve that" and making the protocol secondary.</p>

<p>Now, your question is a recommendation question. The problem I see with this one is that it is very broad and provides not enough criteria by which we could evaluate the answers. Being able to understand Nature, Science and Cell is unfortunately not a helpful criterion, those journals cover a very large part of the natural sciences, not even only biology. I can imagine a very, very large number of possible answers to your question, most of them equally valid. </p>

<p>Now, the question is partially redeemed by the good first answer, that doesn't just dump one recommendation but gives some more detailed advice. The other answers are typical of what you usually find in this kind of question, 1-2 links to possible resources with minimal amount of detail provided. One is even a recommendation for a book the answerer hasn't even read yet.</p>

<p>I'm not completely against recommendation questions, but they should provide a lot of detail and be as specific as possible. This one is just very broad, and questions like this are especially problematic in the early beta. They will be used as an argument to ask similar questions. I probably wouldn't mind this question all that much if it had occured 90 days from now, but for now I think it should remain closed. </p>
 57: <p>As the responsible party for <a href="https://biology.stackexchange.com/questions/27/what-are-the-main-mechanisms-of-interaction-between-the-nervous-and-immune-syste">What are the main mechanisms of interaction between the nervous and immune systems?</a>, I wanted to offer that it differs significantly from a "list" type question.</p>

<p>From the resource <code>yamad</code> cites (I'll grab a few points that are applicable):  </p>

<blockquote>
  <p>Great subjective questions insist that opinion be backed up with facts and references</p>
</blockquote>

<p>It is an active area of research, and can be backed up by scholarly references.  It is <em>slightly</em> open ended, as someone could say "it occurs in X system" and someone else "in Y organ" (I'm being over-simplistic, I realize).</p>

<blockquote>
  <p>Great subjective questions have a constructive, fair, and impartial tone</p>
</blockquote>

<p>I'm not asking what people believe to be the best or their favorite interactions between the two systems, I'm (implicitly) asking what the scientific consensus on the matter is.  With a site like this one, that has to be an assumption that underlies all questions, or else most would be "bad" subjective and have no definitive answer.</p>
 72: <p>I think SE sites are ideal for collecting shared wisdom about quality resources. Questions like <a href="https://stackoverflow.com/questions/562303">https://stackoverflow.com/questions/562303</a> are among the most useful questions on SO for me. Where <em>else</em> can a person get the benefit of a set of experts vetting the best resources to learn from?</p>

<p>My take on perusing SO is that "what's the best"-style questions are closed for being subjective. However, "what are some resources"-style questions are generally not closed. I'm not sure I can put the distinction into words, but I would vote for drawing a similar line.</p>

<p>Then there is also the word from on high: <a href="http://blog.stackoverflow.com/2010/09/good-subjective-bad-subjective/">Good subjective, bad subjective from the SO Blog</a></p>
