The problem with silicone caulk is that once it is on, nothing else will stick to it. You can't re-caulk or even touch up your work without removing all the old caulk and cleaning thoroughly with mineral spirits or other solvent. Much better to use a non-silicone type.
I like the Geocel Proflex caulks, which are a tri-polymer type. Available in clear or colors and in many hardware stores and RV dealers (called Proflex/RV in the RV stores, but it's the same stuff).
For roof repairs, a self-leveling caulk is a good choice. Good brands are Dyco C-10 Flow Seal or Alpha Systems self-leveling caulk. This type of caulk can only be used on horizontal surfaces - it will run down a vertical surface.
Also consider using Eternabond tape to seal roof seams - the stuff is incredible and lasts forever.