How do you remove the exterior roof trim? I think there maybe a leak in the seam between the roof and the body. Does anyone know how to safely remove the trim and seal a possible leak?
If your 06 has a moonroof, then it's more likely it's a clogged drain.
Another common cause for water inside is kicking loose the AC drain hose in the front passenger foot well.
Where to look depends on where and under what circumstances you get water inside.
I think the long thin plastic strips in the groove in front of the roof rack side bars just clips in, should just pry out, but then again I might not remember right.