Quote from Arus;249166:
Tower Cylinder only if you're going purely on the offensive and don't mind losing mobility. Every other cylinder works just fine if you want everything including Summon Golem, Barrier Spikes, Rain Casting, and Shock to be available to you. The only difference between the elemental ones is that you get bonuses for skills of that element, and certain upgrades are only available for certain elemental cylinders. As far as I know, the only time you actually get penalized for using a different-element cylinder is when you use Wind Blast - the maximum distance at which you can push the enemy back is noticeably decreased.
All elemental cylinders positively boost their respective element while decreasing the players effectiveness when using Alchemy skills outside of their element. If you would prefer not to use the tower cylinder, choose a cylinder that has effects that you're particularly fond of.
Wind Cylinder - Wind blast damage (useless) and Frozen Blast freeze duration (very useful at high ranks)
Water Cylinder - Water Cannon damage (very useful)
Fire Cylinder - Flame Burst and Heat Buster damage (very useful)
Earth Cylinder - Barrier Spikes health (useful), Summon Golem status (gamebreaking) and Sand Burst damage (useless)
Cylinder List