Welcome to the forum. I use "Plas-T-Coat" and it works just great. Easy to put on and so far has held up great. I'm sure others may have their favorites. I don't like to use Silicon, because it eventually gets black and looks cruddy.
It just depends upon what your roof is made of. If it is of EDPM or rubber, then you should be sure to use a self leveling caulk that is made for it. Dicor is the best product, but there are others that cost less. No matter what type of roof you have, a self leveling caulk is the best because it will fill in the gaps as it cures.