I recommend to take a positive attitude and just list them in sequence (i.e. reverse chronological, right up front, along with the rest) and say "in preparation for J. Appl. Phys." or whatever journal is planned. Use your common sense. But if you publish all the time in J. Appl. Phys. and know the paper meets the subject and quality hurdles, fine, list that. If you seriously think it is a Science/Nature/Phys Rev paper, than list that. I'm going to assume you are an accomplished paper writer and getting publisheder. Or well on your way to being there. So this should not be rocket science to know where you plan to submit. And you should be submitting to places you plan to get accepted at (not chasing rainbows or submitting junk).
Given that you say "in preparation" or "submitted" or whatever qualifier, it's OBVIOUS that the paper may never get finished (or might evolve, split, merge, etc.) Even "in press" still has some wiggle room in that there is a remote possibility it shifts venue or the like (I mean it's not in the archived literature yet). So what. Not a big deal. Note, I see many CVs on the web that have this exact structure. The simple caveat is plenty. You don't need to obsess about different sections or the like.
The other, not insignificant, benefit is that it concentrates your mind. And makes you more likely to finish, submit, get published. Because you have identified the target.