Red(splash) and lime(chain hit) are great for killing multiple enemies.
Blue(slow) are good for slowing down enemies but since u create water pools well u got the point.
Purple(reduce armor) and cyan(stun) are very effective in numbers vs any type of boss.
Orange(mana gain per hit) well if you play the hidden lvl u can get the maximum mana at 3,195,448 well lets just say 3 million in other way in other missions i didint find them that effective yet still its a powerfull game.
Green(poison) very effective vs low armor and boss waves.
Yellow(triple damage) its power is best vs strong units i soggest combinig it to the maximum if possible.Yet u still need other gems since fast mobs get of range.