Some good tricks already mentioned, the two I might add are: have an assistant do the sighting for you, or use a mirror flat on the surface as an alignment aid - drilling through the hole in a CD can work.
Interesting you find drilling horizontally more accurate xy - I always try to drill vertically ! When chairmaking, the accuracy needed is much better than within 2mm in 3" ( =D> love the mix !). A chair stretcher might be 18" long, and more than 6mm out over that length looks very conspicuous. I use a pair of squares as AndyT suggests, or a square and a sliding bevel for angled holes - but only if it isn't possible to jig/prop the workpiece so that the holes can be drilled vertically.
Last thought: Scotch eye augers can be easier to sight, being long, and easier to turn without wobble than a brace. Although I feel slightly ashamed of myself for doing so in the light of Clico going under, I bought Japanese made single flute augers from Dieter Schmidt recently, and they are very nice to use, and leave a clean hole, and less than half the price of the Clico ones.