Tub drain box - I have broken out concrete (that was uneven). I plan to clean it out a bit - put sand to cover pipes - then level off with concrete.
Toilet hole - floor leveler on this to make smooth (there is a pretty solid cap or something that has some cardboard on edges - it seem pretty solid (supported my weight when I stepped on it).
Pipe for sink drain - cap off (in fact, I have already cut it down a bit and put a cap on it to see if it would change plumbing in my house (did not / almost seems better). Will put cap on with PVC glue.
In a perfect world you would normally disconnect this whole bathroom group from the main drain for proper abandonment of the piping below the slab. What you have are a bunch of dead legs on an open drainage system. This isn't a horrible thing, and as a plumbing engineer I have seen contractors do it both ways, but an inspector would have you cap off the line that feeds into the active drain line, which of course is expensive and requires additional saw cutting of the slab. If I were in your shoes and doing it myself, I would cut the pipes down to at least 4 inches below the finished floor elevation, caps off the pipes making sure they were solid and secure, then just concrete over them like you descibe and call it a day.