well, i'll chime in a different perspective... i wear makeup daily - concealer under the eyes and powder/foundation, a bit of eyeliner, and lip balm, at the bare minimum. i don't have bad skin, but it's not dermatology-perfect, and i just feel more confident with makeup on. when i'm not wearing it, people remark that i look tired (not evaluators... just friends, classmates...). so i've worn makeup daily throughout my "nice clothes" rotations (peds, medicine, neuro), and have never had anyone comment on my makeup or appearance in general. i always err on the conservative side, which i think is just a good rule for professional dress in general. the trick has been with "scrubs" rotations - in ob/gyn, a lot of the female residents seemed to "dress up" more, wearing makeup whether on L&D or in the OR or whatever. in addition they wore a lot more jewelry too (bling on the finger and in the ears), so i tended to wear a toned-down makeup and some plain pearl/diamond (CZ) studs while there. on surgery i was a bit more uneasy about the makeup situation, so i started out not wearing any, but then had both an upper level and an attending who wore makeup to work, so i ended up doing a very bare minimum makeup there.
from the amount i've just rambled about it, it might seem like i'm some makeup-obsessed crazy person, which is not true... i just do believe that it's useful to share ideas on these more ambiguous aspects of med school, which are just as likely to affect others' impression of you as your knowledge base (like it or not). in general i think evaluators are much more likely to call out men on appearance snafus than women, because of the risk of sexual harrassment-type attitudes. so the likelihood of getting called out on your makeup is slim.