Epoxy, I have used Threadmaster and Flexcoat. Both do the job well although I feel Threadmaster releases bubbles far easier. As Ben says, syringes make life easy as long as they do not contain silicon. If unsure, get from a rod builder supplier.
Consider a "lite" version of the epoxy if using for fine trout rods and use a few coats. You get a "lighter" coating on the whipping.
For handles I use either 5 minte or 24 hour cure epoxy (Devcon etc) or Araldite. If need ing to construct a reel fitting, I use 5 minute studd as its easier to keep everythiong in place for 5 minutes than 24 hours.