It is always important at the beginning of any fight to establish the ground-rules that will apply. No kicking, scratching, punching below the belt, etc... Similarly in a debate it is important to establish early on what will and will not be available to debate.
For example, it is common practice to disallow Wikipedia as a source of information because of the numerous factual errors and the ability that people have to alter the information at will. But what about other sources of information?
Is The New York Times a reliable source of information? The Toronto Sun?
Generally it is the practice to allow as much leeway as possible in a debate so to as not unnecessarily restrict the information available. It is too easy for someone who does not agree with something to simply attack the source as being unreliable instead of attacking the argument itself. In discussing the events of the 1989 Tiananmen Square protests some Chinese nationalists will commonly refuse to accept 'western media' sources as evidence of the crimes, even if the media sources were actually there, accusing them of bias against China.
This sort of thinking restricts the debate in such a way that the truth is impossible to get at and the debate becomes excessively one-sided.
This brings me to scientific debate. Suppose there is an argument concerning a particular piece of science, for example, cold fusion. What should be available for the two sides to debate over? Some might say that only peer-reviewed material should be allowed. Others might say that anything goes.
Quite frankly, I don't belong to the group of people who say that 'if it made it through peer-review it must be true!'. There have been numerous cases where scientific inaccuracies have been published in prominent peer-reviewed journals, or cases where contradictory claims have all been published. (The key with those links is that some predict that moderate drinking has no effect on breast cancer rates or increased risks depending on who you speak to) So just because something is published doesn't make it fact. Moreover, the reverse is also true, just because something isn't published in a peer-reviewed paper doesn't automatically make it untrue.
If one is to have a proper scientific debate there can be no sacred cows. Any scientific analysis should be open and available to debate with. If one limits the debate to only peer-reviewed materials it excludes important information sources like government reports, company reports, internal documents from research labs, or expert opinions and summaries. None of which are peer-reviewed but all of which can provide important insight and information to add towards a scientific discussion, especially when such sources of information are properly referenced.
The only time red flags should start flying is when someone is referencing someone who did not properly reference their claims. For example, someone saying 'studies show that alcohol reduces the risk of breast cancer in women' and not referencing it at all, or referencing someone else who doesn't reference their claim should raise a red flag.
Naturally scientific debate also involves a great amount of time. Claims are checked and compared against the references proposed. References are checked for support and contrary articles are looked for. The debate is restarted and more claims are made and must be checked again.