Theoretically, you can use any printer to print on transparencies. Make sure to use the appropriate medium for your printer: laser printers use different transparencies than inkjet printers, for instance. In practice, I use only high-resolution inkjet printers, because the resulting transparencies have a significantly higher contrast than laser printers. I have an Epson Stylus Photo 2200 inkjet printer that supports six color primaries (six different ink cartridges). This model is discontinued by the manufacturer, so I bought mine on craigslist. You can probably find them on ebay as well.
Make sure you install the correct printer driver (don’t use the standard Windows driver), print with a high resolution (at least 300 dpi), using photo-quality settings and with all “automatic” options turned off. The photo-quality setting results in a lot of ink to be deposited on the transparencies – let the print dry for a while (at least 10 minutes) before touching it. You can further regulate the amount of deposited ink in the advanced driver settings. For best results, I use a little less than the regular settings (otherwise saturated colors sometimes end up as ink blobs on the transparencies). My driver settings are like this:
Warning: the above procedure does not correct for the nonlinear gamma and gamut mapping that the driver will automatically introduce. I’ve spent a lot of time trying to calibrating linear responses for this printer and eventually gave up. The closest thing to a radiometrically-corrected print I found is to print from PhotoShop, let it handle the color management in the PhotoShop print settings as seen below.
There are limits to resolution and contrast that you can achieve, even with the best photo printers. When it really matters, we use professional print services. In particular, we highly recommend pageworks.com. The folks at pageworks are extremely helpful and the turnaround time is just one day. They can offset-print transparencies with 5080 dpi; make sure you specify “positive and emulsion up” as options for your order. Pageworks only supports binary black or white patterns in .pdf, .ps, or .eps format. If you want color transparencies, the best place (although not quite as high-resolution) is bowhaus.com. You can order positive or negative RGB transparencies using their light valve technology (LVT). Basically, they expose a photosensitive film with your digital images at resolutions up to 2032 dpi.
I experimented with printed transparencies a lot, using them or custom color filter arrays in home-built cameras, parallax-barrier masks for glasses-free 3D displays, and also for our Layered 3D displays: