Preparations
First, at least three of your characters (I used Squall, Zell and Irvine, but it doesn't really matter who you use) must have as much HP as possible. Over 9000, and you'll be fine. You need lots of Curagas, as powerful attacking magic as possible (Thundaga is fine, but of course, Ultima is better), some Full-Lifes (maybe you don't even need them, but they're good to have), and quite many Shells, Protects and Triples. You may also need a couple of Esunas. All your characters must have Magic-command, at least one should have Item-command and GF:s may also come in handy.
The first battle
Then, you go to Ultimecia's room on the top of her castle. Ultimecia chooses the three characters you use, but don't worry if you didn't get the ones you want. If someone dies and you don't revive him/her right away, he'll be "absorbed into time" and you get a new character. At first you get to fight Ultimecia's human-form and she isn't very dangerous. Keep attacking her with Thundaga (you don't need to waste stronger magic) or GF:s (Diablos is good) until you have your three best characters in use. Then cast Triple, Shell and Protect on them all. Keep those on all the time or you'll get in trouble. If someone gets KO'd, revive him immediately if you don't want to play with just two characters (you probably don't). Keep attacking Ultimecia with triple-Thundaga or GF's and soon she'll summon GF Griever to fight for her.
The most powerful GF
Griever is a little harder, but with Shell and Protect you'll be OK. He has an ability to blow away your magics, so just hope he won't took the ones you need. He can also draw magic from you and cast it on you. Keep using Thundagas and GF:s if you want. Remember to cure if needed. Soon Griever will make his ultimate attack Shockwave Pulsar, which is quite powerful but if you have Shell you'll survive from it. Triple-Curaga after it and you'll be fine again. Then attack (and cure) until you beat him.
Ultimecia-Griever
After beating Griever, Ultimecia will junction herself to him. Don't worry, this may be even easier than Griever. You can't use GF:s anymore, but triple-Thundaga is enough. Ultimecia-Griever's best attack, I think it's name was something like Mega Attractor, looks a lot like Sephiroth's Supernova but Supernova is much cooler and stronger. It's not dangerous, really. Cure when needed, and at some point Ultimecia-Griever's lower body will fall apart. She then uses only physical attacks and is even less-powerful. Keep using triple-Thundagas and at last, Ultimecia-Griever will explode.
Ultimecia
Finally, you get to fight the true Ultimecia. Her Hell's Judgment- attack leaves all of your characters only 1 HP, so triple-Curagas are necessary. If you forget that, she's not very dangerous in the beginning. Ultimecia can also blow away you magics like Griever. Now you should use as powerful attacking magic as you have. Triple-Ultima or -Meteor is probably the best. At first, you can also use Meltdown to lower her vitality. Things get a bit harder when Ultimecia's lower body becomes also a target. It contains Apocalypse, a magic stronger than even Ultima, and Ultimecia will soon draw it from it. YOU can also draw it, but there's no need to. If you want, you can kill the lower body. Then Ultimecia can't use Apocalypse, but she starts using Ultimas very quickly. And because you probably don't want Ultima right after Hell's Judgment, I think you shouldn't kill the lower body. Keep attacking only the upper body. Remember triple-Curagas when your HP falls too low, or you're get killed by Apocalypse. When Ultimecia starts talking you know she'll soon die, so keep attacking. And then, finally...