This was the game that finally had me cave and acquire a Razer Naga. The mouse keys are assigned as the second hotbar, the first hotbar is the default. The mouse is paired with an old Anansi keyboard, which has the macro keys assigned to the third hotbar.

I bundle combo keys together, have them divided into AoE and single target where appropriate, and other actions are assigned where it makes sense depending on job. The least accessed skills tend to be on the latter half of the first hotbar. I have small hands, and it's just physically easier to keep the most used stuff in a certain radius on the left side of the keyboard. Those least-used skills on the 8-12 area of the first hotbar I might click with the cursor, during combat, depending on what else is going on.

Cross-class skills and similar skills are placed on the same keys where possible (for example, Esuna is always 5 on the mouse buttons regardless of which healer it is). Organising this way is one of the ways I've improved at playing, making up for other short comings I might have.

Function keys are as default, and allow easy access to the party list when healing.

I move with either keyboard WASD or mouse buttons, depending on what's going on. For flight, for example, I hit the space bar to take off and then use the mouse to control the rest. Leaves a hand free for my ever-present cup of tea, arguably the most important part of the set-up.