The Bahamut vs. Alexander fight in FFIX is a highlight for me with summons. Very cool. Speaking of cool, the transforming ones of FFXIII are neat too, but I think the game that incorporated summons into the game the best was FFX. The way they were implemented into the battle system was to my liking too. Out of them, I'd say Anima is my favourite as well, but Shiva ought to get an honourable mention.

I will say this about FFX's summons though. Worst. Bahamut. Ever.