Gluby I would love to hear more about this. I fell in love with end grain the first time I saw it. I've always been curious to know how you can reclaim a beam without wrecking your planers and saws on the 1000s of nails.
If you want some good ideas on how to finish your end grain flooring check this site out:
http://www.atdg.com/v2/fr/t-parquet-pav ... debout.htmIt's a french site but the pics say it all. Alot of these guys don't use any filler at all, if you are looking for a nice rustic feel. The beams have rounded corners. The pieces are bevelled and installed like ceramic tiles, so you could get away with just using a buffer to smooth out the edges before finishing. If you go this route your subfloor needs to be flat.
If you have oak, I would definately put a stain on it to reveil the ray flecs. Being a woodworker, you probably know what I mean. It's like a quartersawn effect but even better!