Recently I made some very nice plastic counters for myself using the ship images from the cards. They are only 2D, but have the actual hex as a base (which I quite like) as opposed to a box shape. I brought one to GenCon and measured it against the map they were using for demos. The miniature was a very good, if not quite perfect, fit.
I heard of someone else doing that this year, I've been contemplating it myself actually. Any pitfalls you can warn against for myself or anyone else who'd like to give it a try?
Here is an example of my ship counters:

I simply used SnagIt to copy the images out of the pdfs as a glorified screen grab. Still using SnagIt, I made the background transparent and carefully set the threshold so that it would leave the ship outline untouched. I believe a threshold of 15% to 20% worked for me. I then saved the completed image as a .png to preserve the transparency.
Power Point was used to set up the basic hex pattern. I used the AutoShape hexagon and set the height to 3.25cm and a width to 3.75cm. I colored the turning Hex blue, but if I were to do it again, I would choose Red, since it should stand out better. The laminate seemed to darken the colors such that blue and black were similar.
Once I laid out all the ships that I intended to use, I printed the ships on good printer paper. I took the printed pages to a FedEx/Kinkos (actually Office Max) and asked them to use their heaviest laminate.
To cut the minis from the sheet, it is best to use a nice heavy pair of scissors. I started using what I thought was a nice pair, only to have my hand go numb half way through. I picked up a nicer pair from the hardware store that claimed to be good for vinyl tiles. They looked like a heavy, but regular, pair of scissors.
The resulting counters feel almost exactly like they are heavy plastic punch out counters. I am quite pleased with them. The only complaint that I have would be that they reflect a lot of glare and can be difficult to read at times.