I use the cube bombs the most. It's easy because they stuck and don't roll off. I use the round bombs when I take out enemies inside the skull shaped camps. It's fun to toss bombs inside and watch the enemies running up to them and then....boooom!
Square bombs, because I find more often that I need the bomb to stay in just the right spot.
I think it all comes down to whether you're using bombs for combat or for special projects. Sphere bombs are better for combat, but I rarely use bombs for combat due to the low attack power. I'm more often trying to blow up a wall or cooking up some crazy shenanigans.
I hate them both equally for how many times I accidentally blew myself up trying to mine ore. (including falling all the way down dueling peaks) But seriously the only difference is one rolls and one doesn't, it mostly comes down to which shape you like best. o-o