I think I just figured out how the Eye-Fi and the D60 talk to each other. There's a one byte file on the card, next to the RSPM, RSPC... files called simply 'status'. You need to create it, but once it is there, the card will fill things into it.
When no pictures are pending for upload, it has a 0 in it. I've also seen it at 4 and 5. My guess is that 4 means "trying to upload" and 5 means "failed to upload, not trying any more". I'll have to explore more to be sure.
The D60 can read this file and keep the card powered up as long as the card is trying to upload. As soon as the upload finished, a 0 appears in the file, and the D60 knows to power it down.