I too have had success using water based polyurethane. I dip my pens into the poly, then let hang overnight before re-dipping. I normally put on two coats, but sometimes as many as four if the wood has lots of open grain. When finished dipping, I use the two finest micromesh pads to smooth out any imperfections.
A friend of mine, who doesn't like to wait overnight between coats, developed a "tree" made of dowels to hang pens from after dipping. The tree fits inside a large cardboard box, and he puts a light bulb in to warm the drying blanks. He can put several coats on his pens in a single night.
There is at least one tutorial in the library on dipping. If this sounds tedious, you might try wipe-on poly.