Well I hate to say it, but from what little I know, there are no secrets. No eye of knute mixed with gopher fur, and brushed on with a feather of eel, to make a wood repair joint vanish. Instead, if you don't want to see the joint, the two pieces have to fit together perfectly so you don't see the glue line. If the glue leaves a line, you'll see the joint. Simple concept, and it just takes lots and lots of fitting.
For glue, sometimes I use Tightbond, various two part epoxies, and sometime high quality super glue made for wood that I get at the local wood workers store. The choice sort of depends on the size of wood being glued, and what sort of load it will have.
For color, I use Laurel Mountain Forge stains, Transtint dye, Drop Black, and sometimes asphaltum. For the finish, I like using Classic Gunstock Finish, sometimes with a bit of turpentine in it, and sometimes with some of the previously mentioned colors in it, to try to match the existing finish on the gun.
For metal color and finish, I use the same stuff everyone here does.
For light, I use Daylight color fluorescent bulbs overhead, a 500W halogen when I want a lot of light, and a small spotlight for raking light.
Keep in mind I'm just an amature at this sort of stuff, but the biggest secret in learning to make a perfect seam or joint or color match or texture is lot's of practice.
John