Percentage Damage is very good in many ways. First of all it let's you clear pretty fast because jungle monsters have a lot of health. Second It scales into late game, the later the game goes on the more health you enemies will have, this way you will actually deal more damage as the game goes on. Also, if you are having a smite war with someone who doesn't have percentage of missing health damage you can combo that skill with you smite and out smite the other jungler.
On champions that do have percentage damage, you should make sure you get an item or two that gives you penetration, just because it's percentage doesn't mean they can't block it. The penetration will make sure that the percent will do it's damage.
Some jungle champions that have percentage damage are: Elise ( Q ), Lee Sin ( Second Q ), Kha'Zix ( Evolved Q ), Vi ( Third basic attack with W ), Zac ( W ), Amumu ( W ), Dr. Mundo ( Q ), Evelynn ( R ), Nasus ( R ), Jarvan IV ( Passive ), Volibear ( W Active ), etc.
Penetration items I suggest are : Last Whisper, Black Cleaver, Voidstaff, Liandry's Torment.
I hope this helps!