Having owned and used both cameras (and both systems over the past decade):
Price: You have to factor in the cost of lenses here as well, and depending on what you want to do photographically–say highly compressed (long telephotos), very shallow DOF portraits–a 5D-based Canon system may actually be a good deal cheaper. If you want to make use of a wide angle perspective correction lens, Canon offers the only solution. Price is seldom as simple as the cost of the body.
IQ: Here the 5D wins on the strength of its higher resolution, greater DOF control (yes, even when you want
more DOF, that's better accommodated with a tilt/shift lens where one doesn't have to compromise sharpness for DOF), greater dynamic range (particularly evident in the ability to recover 'blown' highlights),
Noise: Presuming one would like to have one's high ISO shots as free from noise as possible, technically the 5D wins easily. However, this too is a complex discussion as many feel the grainy, 35mm-film-like noise structure of the D200 is aesthetically more pleasing than the 5D's smeary dots of chroma noise–and this is true if the goal is emulation of the look of 35mm film at the same sensitivities. But, in the instance one actually wants the cleanest possible image with the most detail possible, the D200's grain-like noise can't be cleaned without the loss of detail simply because it is indistinguishable (to the software, at least) from genuine image detail; on the other hand, the chroma noise of the 5D can be virtually eliminated with almost any NR software without reducing detail at all. So, for those wanting their DSLR to replace a 6x4.5cm medium format SLR, the 5D's approach yields clean, detailed images at high ISO that are very similar to high speed film scans from medium format.
So, one's assessment of the strengths and weaknesses of either model's noise performance should be based upon one's own needs and experiences, rather than on objective measurements.
Speed: D200 mostly wins here, except that the 5D takes noticeably less time to show and image after capture, and clears its buffer faster.
Build: A dead head in terms of actual quality of assembly and materials. The claims of superiority are based on subjective reactions to ergonomic differences that have virtually nothing to do with the ruggedness of either body. Both are durable cameras with alloy chassis, magnesium-and-plastic exteriors, and shutters designed for a minimum of 100,000 actuations–twice that off ordinary DLSRs. The D200's principle advantage in terms of build is in its adoption of numerous rubber seals to achieve a higher level of weatherization.
AF: A dead heat. Where the D200 excels in motion tracking, it fails in reliably, speedily acquiring focus in low light with only moderately contrasty subjects. Where the 5D is quick and accurate in low light with less contrast subjects, it's not as capable in tracking moving subjects–especially at close range. This is another paramter in which one's own shooting needs will determine the winner more definitively than will any attempt at objective assesment.
Flash: Nikon has an edge here for ease of use, and consistency of automated results. Canon, however, has the better system overall, in my opinion, because its automatic results are 8/10 the same, but it is far easier to control manually with two caveats: no PC sync terminal on the flashes, and IR wireless triggering instead of radio triggering.
Lenses: Both manufacturers make excellent lenses, but the 5D gives you access to a much wider range of choices, particularly at the wide end where one has myriad choices among fast zooms and primes ranger than just a handful of moderately fast zooms. On the long end, the D200 (and any other APS-C sensor camera) gives you more effective reach with less expensive telephotos, though at the expense of diminished ability to limit DOF and isolate subjects from their background.
FF vs DX: Yep, only the individual can decide the relative strengths and weaknesses. However, a great many of these other parameters are related to this fundamental choice, so...
Viewfinder: 5D is bigger and easier to confirm AF on, or to manually focus with. Brightness is about the same.
Ergonomics: Inherently subjective, and can't be quantified as an advantage for either as ergonomics is inherently subjective, and any control arrangement (whether Canon's, Nikon's, or Sony's) can be quite easily mastered with just a little dedicated use. Personally, I find Canon's ergonomics more intuitive than Nikon's, which I bemoan for its reliance on two hands to change most settings that can be accomplished single-handedly on the 5D. Both have their fair share of functions embedded in menus; the distinction will be made on which brand has more of your own most needed functions readily available or buried in a menu. On this point, form your own opinion rather than rely on the experiences of others.
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Kabe Luna
http://www.flickr.com/photos/kabeluna/ 
-Joe
