There are some nuanced differences covered at the below link, but for the most part skull trap is as good as fireball, and better after 10th level. Hold person is another nice third level mage spell if (like me) you consider the priest class largely wasted and can find the scroll. If you really love fireballs though your best bet is to do the import trick (or CLUAconsole) with a few arrows of detonation; then you can drop four fireballs/round with just a couple fighters specced in bow.

Believe it or not though, I tended to avoid area affect spells because once they announce your presence enemy wizards and clerics are free to start casting, and you cannot get in a backstab unless you want the stabbers to take damage, too. Usually I just had my paladin and/or F/M pepper the mages with specced poison arrows while my F/T and straight class thief stabbed a fighter and priest; battles usually ended quickly after that, because the mages were quickly out of commission, slowly dying, while I double teamed their badly wounded meleers.