i find that the word clean usually means it will come on softer, it will creep up, and as said above generally means good qaulity mdma. the come down, as in when the effects are wearing off, will be smooth, ie, you wont really be able to tell for sure that you have 'come down', while other pills, you will get very sleepy quickly, or just feel like shit very quickly, this means the pill is not as clean.
i think an example of a good pill that was not clean was the green BB of last year. for me it was very dirty... extensive jawclenching - far beyond normal levels, a very strong headfuck (for me anyway) and a difficult couple of days afterwards.
whilst a recent pink heart could be described as clean. comedown virtually non-existent, following days were not difficult like i was not burdened by having had it, the roll was strong but not a headfuck.
its hard to describe. a pill that is not clean may mean that during your roll you have longer periods of discomfort (by that i mean the restlessness and feeling of 'i dunno what i wanna do' that you get from strong doses), while a cleaner pill should have less of these periods if any at all.
i dunno how correct i am, tahts just the way i perceive it, i havent described what i mean very well, but yeah correct me if im wrong!