I installed a floor made from locally produced, 3 1/4" hard maple. There are a few gaps under 1/16th of an inch that I don't like. I normally buy the best product for the application, but the stores will be closed tomorrow. What I do have access to is epoxy. Most wood fillers are a two part epoxy anyways. One video shows epoxy mixed with sawdust to fill knots and cracks. Gaps seem a little different, though. Will mixing up a thick sawdust-epoxy paste be a definite, long term, aesthetic improvement? The floor isn't sanded or finished yet.
The epoxy glue products are not made for this situation. It will stick out like a sore thumb. It will not accept stain. There are any number of good quality wood filler products that are made specifically for this application. The manufacturers of these products state that they will accept stain however, I have found that to be only partially true. They are still the best choice for this job. Wood that is properly seasoned and good tight installation is the best defense against having to fill the cracks.
I used contractor-grade wood filler (specifically, Elmer's ProBond Max) along all the grooves between beams in one room that I resurfaced using a dark stain, not knowing for sure how it would turn out. Although there were some spots that had to be re-patched after the floor sander shook some filler loose, I did end up with a result that I liked a lot - to the point of wishing I'd done the whole house that way. (Whether it's more attractive is quite subjective, but it definitely is easier to keep clean.)
There are some caveats though. Even with water popping, the filler absorbed more stain than the wood. So I do have darker lines between beams - it's just slender and subtle enough that you have to get down to the floor to see it. I even had some gaps up to 1/8" (and maybe more) that I also patched, and they are more perceptible but still not ugly.
I also tried mixing my own filler with wood or white glue and dust from the floor, but had too much difficulty producing a substance with usable consistency. If you need to match natural wood grain, this seems to be the conventional wisdom* and I know no better alternative. If you're staining, you might as well take the easy route and use general purpose wood filler. In either case, you should expect that the filled area - even if it matches hue quite closely - will be darker.
*For more detail, see: https://woodworking.stackexchange.com/questions/5873/making-wood-filler-from-sawdust