My 97 Tahoe had a slow leak in the back that I would discover by the carpet being wet after rain. I finally tracked it down to the 3rd brake light mounting holes on the roof. The gasket had deteriorated and there were two gaps, allowing water to easily run down the two square mounting holes in the roof. I needed to replace the 3rd brake light anyway, which came with a new foam gasket. I added a little bit of silicone around the edges of the mounted brake light. We'll see how it fares in the rainy winter...
Years ago, I also had leaking rain water coming through the back hatch, a consequence of pine needles (Pacific Northwest) working their way between the hatch and the roof rubber when opening and closing the hatch. It was causing the little rubber lip to fold in on itself, thus allowing more pine needles in to break the seal in multiple places between the window and the door rubber. The fix was to get that little rubber lip in the right position, then tack it in place with silicone, holding it in place against the roof. It permanently (for at least a decade, now) solved the issue on both my 97 Tahoe and my parents 96 Suburban.