Squeegee technique and not stretching the vinyl is most of it. Go slow and firm. If you have a big piece, roll it up so it doesn't sag. A big squeegee can be troublesome. I use the standard size gold ones for everything. The cheap squeegees will wear out and eventually form a curve at the blade.
Some plastics and finishes will outgas and bubbles will form even after a perfect application. Usually, they will settle down (especially after a few days of outdoor exposure). Temperature also makes a difference; try to have both the surface and the vinyl at the same temperature (room temperature is ideal). Really cold vinyl is rigid and less conforming, really hot vinyl will be soft and stretch easily when applying. I do not recommend applying vinyl at temperatures lower than 50° f. Also, if you store your vinyl in a cold environment (unheated warehouse, garage, maybe the vinyl was shipped in the winter), let it warm up to room temperature before using.
Also use a good quality paper transfer tape. Plastic can cause all kinds of problems, usually related to static (convenient for overlays; I use registration marks strategically placed or a light table).