They can be nice side items to certain units. Such as a scout, just in case he gets spotted. Particularly Pangaeas and Caelum scouts which can fly so they end up quickly near the enemy commanders. Kindof a kamikazi strategy for "in case you are caught".
Ive also tried it on some seducers when I find that Im failing often and ending up in one-on-one combats which I lose. It can help to keep the other equipment on the unit from falling into enemy hands.
I've used them with solid success as Pangaea's harpies and attack archers. Fire gems aren't good for a whole lot, IMO, and its a good a use as any. One tool is using them to attack near where an enemy has been putting his mages- with luck a few will explode, and 3 gems is a reasonable price to blow up a mage or two.