First time through, I used them in big battles against bosses, and when I was really in need of some help to get out of a jam.

Nowadays, I barely use them, as my use of the sphere grid is much much better. I pull out Bahamut almost exclusively, if only for fun. I gave him some extra abilities -- like Full-Life, Zombiestrike, and Curaga. This way, he has, in addition to highest level magic, he can also use white magic and be a totally self-sustaining character in his own right. Leveling up the Aeons (via strength, etc.) is too costly of items that are better utilized on the regular characters.

I imagine once I get Anima and Magus Sisters and make my run at the monster arena, I will have to use them... however, my characters are developing nicely, so it may not be an issue.

I think it comes down to how well you utilize the sphere grid w.r.t. the main characters.