We recently completed a project with white oak floors stained almost black with three coats of an oil based finish. All surface scratches show up light colored, making them very visible. What is the best finish to use on black floors and what do you recommend we do to make these floors more durable?

Well nothing is going to be impervious to this type of wear, but to reduce the visible appearance of these scratches, you could buff and coat the floor with "Street-Shoe" matte finish, from BASIC.
A better plan for these dark floors is a combination of preventative maintenance and fastitious cleaning program

Last year we stained an existing oak floor completely black which turned out to be quite a lengthy process. We decided to finish the floor with Bona-Kemi's Traffic. The floor still looks amazing but does require a bit more up keep then most other floors we've done in the past. Old English for dark floors works well against those light scratches that may show up. Truly a gem of a floor.

Here is a pic (pardon the quality):

Here is a bigger pic: