What is the best way to apply super glue (cyanoacrylate)?

This really depends on what it is you plan to glue, most things can be glued straight from the bottle, but this will give you quite a large bead of glue on application, which may be more than you need and cause an over spill on your model leaving an unsightly amount of glue on the seam.

Some modellers will use a cocktail stick/toothpick to add a small amount of glue. There are glues that come with metal needle type applicators for precision work and there are also disposable plastic tips for certain brands of super glue such as Roket which allow for a precise delivery of glue.

You can also use syringes to deliver just the right amount in  the right place.

There are also microbrushes which are equally as good.

I personally use all of the above to allow for every eventuality. It all comes down to "the right tool for the job".