For dark seeds, I think it depends on why they're dark.
I had no trouble at all sprouting tomatoes I received in a trade once where every seed of the variety (which was coincidentally named Black) was dark. When I saved seeds from my Black tomato fruits, the seeds weren't dark; so, I'm guessing it was stains from the fermentation or something. From my own saved seeds (and I save a *lot*), I've only had a batch of seeds be dark like that once that I recall, and that was with an overripe Black from Tula fruit (every seed was dark; they were dark without fermenting them; I haven't tried sprouting them, but I suppose they will sprout). My guess is they just experienced some weird fermentation or staining in the fruit or something. As long as they're not rotten, they're probably fine. Taking the seed coat off may reveal things. I'd take precautions against disease anyway, though (just in case; I zap my seeds with a Z4EX; some people might soak with a little bleach or hydrogen peroxide; some people might re-ferment them).
When seeds rot, it usually starts with a spot on them, rather than the whole seed being dark, in my experience (it sounds like even some of those with spots might sprout, though!). If the whole seed is another color, they may be fine. Some tomato seeds are other colors besides dark and the regular tomato seed color. Most seeds are normal under a UV flashlight, but I've noticed that a certain percentage of them seem to get the same look that a milk jug gets under UV light (but it's just the color; the seeds can sprout). I wonder if those seeds block UV rays and are capable of staying viable longer in the sun.
Anyway, as my experience with dark seeds is limited, take it with a grain of salt.
