Preferably not actual silicone. It seals okay, but if it ever needs replacement or touching up it's a long, hard process as every bit of the old must be removed. Pretty much nothing sticks to cured silicone, not even more silicone.
Geocel Proflex RV is the "standard" sealant for this sort of thing. There are other polyurethane sealants that are very similar and perhaps more readily available for less money; I've used OSI Quad from a big box store with decent success. Somewhat less standard, but in my rather limited experience also effective, is to use plumber's putty under small attachments like clearance lights and cargo bay door holders.
3M 4400 would be another good, tried-and-true option. 3M 5200 would also work, but you'd pretty much never be able to remove the lights if ever needed.
