Misconceptions about the purpose and usage of Pantone are to be expected, since very few graphic designers are regular Linux users (much less coders). The legal issues, on the other hand, are probably kept intentionally murky by Pantone to discourage others from competing. Let's take a look at both.
We don't buy colors, we buy peace of mind
Pantone's bread and butter is the Pantone Matching System¨(PMS), an ink-matching system widely used by designers and printers for color reproduction. To use it, you must buy a Pantone swatch book -- a printed and bound collection of cards containing hundreds upon hundreds of colored rectangles labeled with identification numbers. When you design your business card or garage sale poster and need an eye-catching mauve to really make it stand out, you find the color you want in the swatch book and give its number to the printer when you drop off your finished design.
The printer looks up the number in his Pantone instructions, and mixes a special ink for it with Pantone's recipe (which includes inks outside traditional RGB color models, including neons and metallic finishes). If everything goes according to plan, the finished product and the card you chose at the beginning look the same.
Nowhere in this process is special behavior required of the software you used to create your design. Nowhere does the phrase "Pantone compatible" or "Pantone compliant" arise. That's because the crux of the system is the printed swatch books and the printer's instructions. Applications such as QuarkXPress and Adobe Photoshop may have a list of Pantone numbered colors available through their built-in color chooser, but they also warn you that what you see on screen is not guaranteed to match the printed output, and refer you to the printed swatch book.
It's also important to note that Pantone Matching is for spot colors only, or colors that don't blend with the other elements on the page. You can certainly choose pretty colors out of the swatch book to paint with, but you've then left the world of spot colors and entered CMYK. Pantone Matching is no longer involved, and you must rely on calibrated displays and printers to match colors.
That said, many people choose colors from Pantone books even when working in CMYK because the books are a good reference; using them yields far fewer surprises than picking colors from an RGB monitor.
Think back to that Photoshop color chooser. It presents a list of numbered colors; when you select one, Photoshop changes the active "painting color" to an RGB value that is as close a match as possible. "If that's all that happens," we wonder, "can't the GIMP, Inkscape, and Scribus do the same?"
In theory, yes. If you search the Web, you can find homemade colors and palettes for many graphics apps that refer back to the Pantone numbers. The holdup is that an application that packages or ships a color palette derived from the Pantone swatches runs the risk of legal action from Pantone.
Exactly what legal action Pantone would take is unclear, but its "About Us" Web page claims that "an unauthorized claim by third parties either as principals or agents, inferring that any referenced color or color system is the same as, or equivalent to, a color standard or color system of Pantone, may be a violation of Pantone's proprietary rights" -- without being specific. Is it patents? Copyrights? Trademarks?
It seems as if the company is being intentionally unclear; certainly by doing so, Pantone can wave a bigger, scarier legal club and chill a wider variety of competition. A Groklaw discussion raises the question of whether any of Pantone's patents apply to the color matching system itself. It is widely agreed that colors and numbers cannot be copyrighted or patented -- though perhaps Pantone would claim that its collection of color swatches as a whole constitutes a "database" which could be copyrighted, much like the phone book.
Certainly the simplest claim would be trademark misappropriation or dilution towards someone who produced a color palette marketed as compatible with Pantone's. This is what prevents open source products from including built-in Pantone color choosers.
Pantone has nothing to lose by licensing use of the Pantone palette free-of-charge, since the company makes its money from printers' supplies and book sales (which aren't cheap, and you are encouraged to replace the books annually to ward off fading and long-term color shifts). Pantone probably has some additional customers to gain by allowing free software to use its technology. But the company doesn't appear interested.
Color me bad
So marketing your own full-blown replacement for Pantone Matching is out of the question, and shipping a palette of colors clearly mimicking the Pantone color swatches puts you at risk for a lawsuit. What's an open source designer to do?
Fortunately, Pantone Matching relies almost entirely on the swatch books to function. Like the secret agents of conflicts past, the only reason your color message gets decoded at all when it reaches the print shop is that you both have the same code book. With a Pantone book in hand, you can tag your designs with Pantone numbers to your heart's content without crossing any legal lines.
Specifically, anything drawn in scalable vector graphics (SVG) format has fill and stroke color XML attribute; with a program such as Inkscape, you can place tags with your desired Pantone numbers into the drawing itself. Thankfully, graphics juggernaut Adobe is a big proponent of SVG, and most print shops will accept it along with Freehand and Illustrator files.
Scribus can do two-color and three-color separations, although it does not build in those functions at this stage. To use them, read the Scribus wiki, follow the spot color tutorial, and output your final product in PDF/X-3 format -- a stripped-down refinement of PDF optimized for professional printing. It's probably obvious, but one-color designs do not need separations.
When you reach four colors and up, however, CMYK and not spot-color support becomes the issue. For that, there is a GIMP-CMYK plugin in development, and Imagemagick and libTIFF support CMYK (with color profiles), but I would not rule out being nice to your printer and asking if their folks would convert the images themselves. In the real world, you'll make multiple trips to the printer for revisions and hard proofs, so you might as well make friends.
Pantone's cloud of legal menace is relevant only to vendors; users have never needed permission or license fees to tell a print shop to output their letterhead in a particular color. I am skeptical of the broad "proprietary rights" claim asserted at Pantone's Web site, but the niche market is so small that I doubt we will ever see a good test case go to trial. If that does happen, the fallout will be interesting to watch. In the meantime, free software users need only educate themselves to work around the inconvenience.