It depends on various things, for me. If it's synthetic line, I've been known to cut it rather short, then melt the last bit of the end down to where it's flush with the rest of the knot.
For a loose knot, i.e., one that has plenty of slack in it after it's completed, I have sometimes pulled enough of the two ends out that I could splice them together and taper the splice to somewhat minimize its appearance. After that, the knot is worked even again, absorbing the slack next to the splice into the body of the knot.
With metal, I either just tuck the ends in and leave them alone, or I cut them flush and solder or fuse them. I try not to do so perfect a job that the customer and his friends can't find it at all, because part of the fun is the discovery that, yes, it really is a knot, and the ends are findable

I tie a lot of cotton turk's head bracelets to give away, and out of a combination of laziness and an affection for added decoration, I usually just bring the ends out and whip or splice or stop-knot them, then fray anywhere from half an inch on up of the ends to make a fluffy tassel past the stop.
Loren
http://www.golden-knots.com/