I personally found red gems are your best friend. They seem to be by far the most effective if you have plenty of traps to slow the monsters down. Also, experiment with multi color gems on a lower level that is easy to beat. I recommend you only go dual color as tri color gems have too little chance of landing the special effects. So i suggest sticking to pure red gems, and combination of yellow green, green lime, or yellow lime. but pure is always your best bet if you can do it.
I like the red gems because of the splash damage, and at the higher levels they definately deal the most amount of damage, and the special on them has a very high chance of working compared to the specials on other gems. But having the traps...and lots of them is an absolute must on the higher levels.
Actually, the difference between red and purple gems...the red 1s have a wide range when their grade is 9+, and the purple ones...IT SHOCKED ME !!!!x_x It's speed is as fast as a machine gun when it's grade is 9+,too.
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.