The limit breaks that can deal the most damage are most definately the multiple hit ones. The characters with the highest hits are as follows;

Cid 4-1 : Highwind (18 hits, 11/16th base damage)
Barret 3-2 : Angermax (18 hits, 1/2th base damage)
Cloud 4-1 : Omnislash (15 hits, 3/4th base damage)
Yuffie 3-2 : Doom of the Living (15 hits, 5/8th base damage)