Yep, proBoolean, floaters or chamfer'ed verts. Oh and... you can also cut in a a rough hole, then use the GeoPoly button in Graphite modeling tools to round out the poly making it circular. Illusion catalyst also has a free script available that does a similar function but works on loops instead of polys. It also makes…
if it is a high poly model i tend to just use floaters, since there quick and dont messy up the model, or the vert chamfer method already shown. with the vert chamfer method if used for a LP mesh, you can just add more connecting loops in step 5 across the square face before you Spherify ti make it more round, just be sure…