Is there a "safe" sub-floor leveling compound?
wood subfloor? can you cut out the bad sections and replace it with new plywood?

if you do this, i would recommend installing some 2x4's underneath the section you cut out, perpendicular to the stringers. install them so they cover the joint between the old and new subfloor. depending on the size of the patch, you might also want to support it somewhere in the middle. and then also install 2x4's along the edges of the patch parallel to the stringers.

below is a drawing that show's what i'm talking about. it's a bottom-up view of the subfloor. the part you're cutting out is in red, and the 2x4's you're installing are in green. i did not draw in the parallel 2x4's i recommended above.