• Latex - Inexpensive - can be sanded and painted - won't adhere to metal Will crack eventually where temperatures vary greatly
• Acrylic latex formulations are more durable.
  It is water-based, so shrinks at it cures.
• Butyl rubber - More flexible than silicone - can be painted after 1 week
• Siliconized latex - very durable and flexible - can't be sanded
• 100% Silicone - Very durable - can't be painted or sanded

Commercial Grade:
I noticed the stuff my roofers used was better than the stuff I got at HomeDepot.

I went to my local Allied Building Products (recommended by a contractor/engineer friend).
The recommended NPC Solar Seal #900 ($7.40 per tube). A premium adhesive/sealant based on terpolymer technology which offers an alternative to silicone & urethane sealants and caulk.
Technical Data Sheet
Ingredients: Resin, Rubber Elastomer mixture (proprietary); Petroleum Solvent; Titanium Dioxide; Calcium Carbonate
Standards: ASTM C-920, Type S, Grade NS, Class 25, TT-S-00230c, Class A, Type II

NPC Solar Seal 900 Adhesive Sealant: Amazon.com: Industrial & Scientific

My local lumber store (Somerville Lumber) recommended Sashco Through the Roof ($8)
Super elastic, Lasts 20x longer than asphalt.
Standards: ASTM C794

On asphalt: use an asphalt caulk.

On modified bitumen (asphalt and a variety of rubber modifiers and solvents.): use a modified bitumen mastic. In critical areas where movement is anticipated, use a good grade of urethane or polyether sealant.

On EPDM ((ethylene propylene diene terpolymer) - synthetic rubber: use a solvent-based EPDM lap seal caulk on splice joints. On flashing: use polyether sealants. Urethane sealants usually don't adhere to EPDM.

On PVC: use a polyether sealant, urethane or an oxime-cure silicone.

On Hypalon (less than six months old): use only fresh Hypalon sealant. On weathered Hypalon: don't attempt to use a sealant; it will probably fail.

On TPO (Thermoplastic polyolefin): use a urethane or polyether only with an effective primer. Carlisle and Chem Link have an effective TPO primer.

On polyurethane foam: use urethane, oxime-cure silicone or polyether sealants.

On most metal roofs: urethane or oxime-cure silicone (non-corrosive) and polyether sealants work well.

On Kynar (polyvinylidine flouride)-coated metal: oxime-cure silicone works well. Urethane does not bond at all to Kynar.

Avoid using caulk on all single-ply membranes.

Source: From Caulk to Sealants | RoofingContractor.com