Some of it is personal choice for the look you're after. These days GOOD LEDs will be as bright and through light as far as halogens.
When it comes to roof lights, you want to be shooting light way down the path so that you don't overrun your lights when bombing down a gravel road. So regardless of the source of the light, be sure to find ones tuned (focal and glass) for driver or spot/pencil.
As for Halogens they will be a larger electrical draw and the light is more yellow (warm). They can put out a lot of lumens. LEDs have a very low draw and the light is much whiter which can seem brighter but may not project as far. Regardless of light source get ones with high quality glass and reflectors. Poor glass and reflectors causes shadows and dark areas on the fringes which will cause eye fatigue after driving for awhile. If you want to see some good lights (HID and LEDs check out baja design)
The other thing to consider, for trails where you are driving slower working through stuff, good flood lights are a better choice. Floods will create a well light wide area so you can see everything that is coming up or your working through. Flood lights work best mounted on the bumper since if they are on the roof, they will cause a glare off the hood and not get to what is right in front of your wheels to help you and your spotter.
I have both roof lights (2 spot, 2 driving) and 2 floods on the bumper. nine times out of ten, I only use the bumper flood lights. The roof lights where great when we went through the Baja, but most of the local trails i run at night are twists and turns and the roof light's aren't all that helpful... but they do light up the trees nicely
whatever way you decide to go. This video will help with the install. Bumper and no drill roof top light install for FJ Cruiser
more details, diagrams and ideas available at
Installing rooftop off,road lights on FJ Cruiser