It seems in general bombs haven't gotten the overhaul like many other items have gotten, sorta. There still has been a variety, mainly in the last few games. The Arrows and Boomerang seem to be different in nearly ever Zelda game but not so much the bombs.
Personally though if I had to choose, I think just the standard bombs from Legend of Zelda, Link to the Past, Link's Awakening, and the various other 'normal' bombs. The bombchus were terrible in Ocarina of Time, way too inaccurate. In Phantom Hourglass the bombchus were cool but just so radically different than standard bombs. THey are up there too, but the classic bomb still is my preference.