The easy ones
Some questions are reasonably sect-agnostic and are unlikely to elicit different responses from followers of different sects. Questions about the life of the Buddha (which is probably mostly agreed upon by all sects, unlike some of his teachings) are likely to fall into this category, as are questions about the historical evolution of Buddhism, and maybe some questions about meditation (among others). So these questions shouldn't cause us too much trouble.
Other questions are obviously sect-specific, and the question asker knows it: e.g. What is the purpose of using a wand to hit a monk in Zen meditation?. In this case, it is obvious what to do - tag the question with an appropriate sect-related tag. At the broadest level, I suppose we have theravada, mahayana, or vajrayana - but there are also finer classifications that may be of use, e.g. zen, pure-land, etc.
I think it is a matter of the questioner's taste whether s/he would rather use one of the three top-level tags or something more specific, though of course we should be open to retagging a question with some other sect if would help the questioner get more relevant answers. Either way, the use of a sect-specific tag signals that the questioner knows what s/he's asking about, and wants an answer in the same vein.
The tricky ones
Then we get to the real mess - questions by laypeople that have vaguely-defined ideas about things that Buddhists do and who are unaware of the fine distinctions between the sects (disclaimer: I'm pretty much one of them). This is the tough part.
Christianity.SE, which is the most mature religion SE site, has declared these questions off-topic: "a survey of all Christian views on a particular subject" and "what the Bible says about a subject (unless you specify a doctrine/tradition)" are on the do-not-ask list. This is going to be a bigger problem for us than for them - because of the demographics of Stack Exchange, we're going to have far more non-Buddhists asking questions than they have non-Christians asking questions (relative to the size of the site).
The site is already full of questions like these - as a rough estimate, I'd say at least half fall into this category. On the other hand, I expect that there will be relatively fewer of them going forward - there's only so many generic questions that can be asked.
The easy solution is to ban them outright, like Christianity.SE did - but I don't know if we want to do that. These questions have tangible value both in terms of growth for the site (i.e. these general questions are the ones that are going to draw the most visitors) and as a view into the different sects within Buddhism that would be difficult to attain if we had to fragment these answers across multiple questions like "How do I attain enlightenment in Theravada?" and "How do I attain enlightenment in Zen?" and "How do I attain enlightenment in Bon?".
I don't know what the best thing to do is here; this is going to take a fair bit of discussion to figure out.
To the easy ones
To sect-agnostic questions
Since these questions are inherently sect-agnostic, it shouldn't matter too much what sect you follow. Nonetheless, it behooves you to make clear where you're coming from. If your answer is based on a passage from the Pali Canon, mention that. If you're drawing on something you heard in a talk by a Zen master, mention that. This helps place the answers in context.
To sect-specific questions.
Well, to start with, you obviously shouldn't answer a question tagged zen with Theravada teachings unless 1.) you have a really good contribution to make, or 2.) the particular teachings you're using happen to be shared with Zen.
Other than that, we should proceed as above - mention what you're drawing your answer from. If it's from the teachings of a particular subsect or a particular teacher, make a note of that in your answer, because, after all, there can be differing interpretations even within a sect.
To the tricky ones
As long as we allow these questions, it is incredibly important that these questions be answered with an explicit mention of the tradition on which the answer is based. It does nobody any good to see a question like "How do I attain enlightenment?" with a dozen contradictory answers and no explanation of why they are contradictory.
I strongly believe that we, as a community, should discourage answers that lack an indication of the tradition/sect/whatever on which the answer is based by 1.) commenting on the answer and politely but firmly asking the answerer to edit their answer with a mention of what scripture/tradition/etc their answer is based on; and 2.) downvoting if, after some time, they have not done that.