I've never found a use for the Ice Cypher outside of a single platforming section and the few blue shielded enemies. Enemies might act as shields, but they also prevent you from actually moving towards and hitting the next enemy.
The Explosive Cypher is the all around best damage Cypher, which is all you really need aside from a few gun turrets. The Magnetic Cypher isn't really very good for the actual Cypher, but the Kunai and Charge are great. You can hit enemies above you easier with it, and it goes through floors, but it seems to have the lowest damage, or tied for lowest with Ice. I'm also not sure why you would bother with Ice Kunai against fliers when the Explosive and Magnetic take them out MUCH faster.
The Magnetic Charge also seems to actually be the best charge of the group. Not only does it disable an enemy, it also draws fire from those in close proximity. So it's basically like an Ice charge (which I never found an upgrade for if it's even in the game).