I play on PC but use PS3 controller because it's way much comfortable. Here are few tips I found throughout FFXIV forums when using PS3 controller

1. Holding (L1 or R1) + (L2 or R2): Cycles your main target through enemies, regardless of what setting you have defined for targeting filter. Tends to focus on the target closest to you. Useful when you forgot what target filter you were using in the middle of a battle.
2. Holding (L1) + (L2): Cycles through the aggroed enemies only. Useful when you want to regrab the aggro on a mob that you can't see on the current screen.
3. D-Pad <-, ->: Cycle through the enemies depending on the target filter you've set. Personally, I only set it to cycle b/w aggroed enemies when weapon is drawn.
4. D-Pad Up, Dwn: Cycle through your party members. Useful for cover.

One thing that I've set up personally was delaying the time needed to sheath/unsheath weapon after battle to the max so that I can have different target filter for the two stances.