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Until a couple of years ago, the choice for Linux users was simple: everyone ran the same old LPD from BSD's Net-2 code. Then LPRng became more popular, but nowadays most modern Linux distributions use CUPS, the Common UNIX Printing System. CUPS is an implementation of the Internet Printing Protocol (IPP), an HTTP-like RFC standard replacement protocol for the venerable (and clunky) LPD protocol. CUPS is distributed under the GNU Public License. CUPS is also the default print system on MacOS X.
Most distributions come with a GUI for configuring networked and local (parallel port or USB) printers. They let you choose the printer type from a list and allow easy testing. You don't have to bother about syntax and location of configuration files. Check your system documentation before you attempt installing your printer.
CUPS can also be configured using a web interface that runs on port 631 on your computer. To check if this feature is enabled, try browsing to localhost:631/help or localhost:631/.
As more and more printer vendors make drivers for CUPS available, CUPS will allow easy connection with almost any printer that you can plug into a serial, parallel, or USB port, plus any printer on the network. CUPS will ensure a uniform presentation to you and your applications of all different types of printers.
Printers that only come with a Win9x driver could be problematic if they have no other support. Check with http://linuxprinting.org/ when in doubt.
In the past, your best choice would have been a printer with native PostScript support in the firmware, since nearly all UNIX or Linux software producing printable output, produces it in PostScript, the publishing industry's printer control language of choice. PostScript printers are usually a bit more expensive, but it is a device-independent, open programming language and you're always 100% sure that they will work. These days, however, the importance of this rule of thumb is dwindling.