This is a little more work than listing them by CP, but what are your top 12 pokemon by pokemon level? If you don't know the exact levels for all of them, and don't want to look them up, just approximate the best you can.
Mine:
1. Lvl 40 Dragonite DT/O 100% CP 3581
2. Lvl 40 Exeggutor C/P 100% CP 2916
3. Lvl 38.5 Rhydon MS/SE CP 3181
4. Lvl 38.5 Gyarados DT/O CP 3175
5 Lvl 38.5 Gyarados (shiny) DT/O CP 3088
6. Lvl 38 Alakazam PC/SB 93% CP 2775
7. Lvl 38 Houndoom S/FP 93% CP 2432
8. Lvl 37 Scizor FC/XS 100% CP2681
9. Lvl 37 Charizard WA/O 100% CP 2571
10. Lvl 37 Kingdra DB/B 100% CP 2320
11. Lvl 36 Mewtwo C/SB 80% CP 3669
12. Lvl 36 Vaporeon WG/AT CP 2921
13. Lvl 36 Machamp C/DP 96% CP 2710
Several of these were powered up when the old gym system was in effect, and CP mattered for gym placement. Some are powered up to important breakpoints. And I believe that useful 100% mons should eventually be powered up to the max. In general, I do two power ups at a time, because I like to keep them at an even level (e.g. lvl 36, not lvl 35.5 or 36.5).
edit: Oops, forgot my Mewtwo the first time. I believe Mewtwos also should be maxed, but I am low on rare candy, and am spreading it around to other legendaries to eventually be powered up.