I think the same goes for disciplined researchers in other fields, too. A good Historian authoring a monograph will have a clearly formed thesis statement, followed by supporting evidence, followed by a conclusion.
While this may be oversimplified for the sake of discussion, the nature of the body of a paper (the supporting evidence) is where one can really pick up on the quality of the research and how well supported the conclusion actually is. Bibliographies or works cited pages should go further than simply the author, work, page number, etc, but include a dissection of the source itself. One would not, for example, cite the Anglo Saxon Chronicles without addressing inherent problems with the Chronicles such as legendary/semi-legendary aspects, religious influences, etc. Boiling down the source (with all its flaws) while still showing the relevance can be tough with a lot of primary source documents.
But a well formed thesis would not simply rely on documents. Archaeological evidence and available data from what I'll call "hard" science must come into play as well. If documentary evidence nests nicely with physical evidence, then you have something. This is where areas like attempting to find the historical "Exodus" from Egypt and the like start to collapse. The documentary evidence (i.e. the Pentateuch) may have some verifiable claims, but the entirety of the narrative may not be supported.
This is where I find the biggest logical problems among many creationist (well, I'll limit that to Young Earth Creationist or Biblical Literalists) arguments. They simply form their thesis ("God made the universe, liberated the Hebrews from Egypt, Flooded the World" what have you) and then declare the documentary evidence -- really mythos -- is itself authority enough to validate the thesis statement. It's the ultimate argument from authority: God authored the Bible, the Bible says this happened, therefore it happened. The same is done with what they bizarrely perceive as supporting evidence: strange hypotheses (such as the vapor canopy) which they simply cannot defend scientifically or historically. They strangely regard the fact that they have been able to form a hypothesis as evidence in and of itself! They stop there, declare victory, and take their family to lunch and a tour of the Creation Museum.
I've seen this same pattern repeated time and time again reading through these threads (particularly IamJoseph's posts) where there is no logical support for what is declared. Simply "X is true. Y says it is true. Therefore X is really super true."
Hopefully this made at least a bit of sense. I'm enjoying a post Thanksgiving conversation with my old friend Johnny Walker. He's a helluva guy.