Four years ago these are the sections on Skinz.org along with the # of skins in that section.
eFX: 173
EGN: 17
Half-Life: 23
K-Jofol: 14
LS Mods: 3
MPFree: 7
MyPad: 9
NeoPlanet: 23
PalmOS Emu: 11
QCD: 23
WindowBlinds: 18
WinAmp: 156
WPlay: 5
Some of these apps I'm not very sure about. Obviously Half-life isn't a skinnable app.
From top to bottom:
eFX was developed by Thirty4. They halted development after signing up with a company called Akamai (http://www.akamaidesign.com/). But nothing further ever was publicly released beyond 0.40 in 1999.
I'm not completely sure what EGN was. But you can find out more about it here (http://www.geocities.com/SiliconValley/Sector/2995/index.html).
K-Jfol was a skinnable MP3 player that was bought out by Winamp. Its technology is thought to have served as the basis for Winamp 3.
Litestep Mods continue to be developed with themes available here at WinCustomize as well as at www.litestep.com
MPFree was another skinnable MP3 player. It has a section over at deviantART http://www.deviantart.com/browse/t/skin/mpfree/.
MyPad was a skinnable text editor. You can find its section at deviantART here: http://www.deviantart.com/thumbnails.php?section=mypad
Neoplanet was a skinnable web browser. It was actually one of those dot-com companies that saw skinning at the pathway to immense popularity. Unfortunately they were a bit too far ahead of the curve. At one point, Neoplanet had something like 60+ employees. It provided a Lord of the Rings web browser as well as an Austin Powers web browser. When the dot-com crash came, they were one of the early casaulties. You can still download their program at www.neoplanet.com (http://www.neoplanet.com).
QCD was another MP3 player. It is still updated on a regular basis.(http://www.quinnware.com/news.html). The most recent release being only a couple days old. It looks pretty impressive too (http://images.deviantart.com/large/skin/qcd/BetaMaxx.jpg).
WindowBlinds has grown in popularity over the years helping to make Stardock a significant player in the customization community. In 1999, the company was struggling in its transition from OS/2 to Windows. Stardock was in the process of creating Object Desktop for Windows and having a difficult time with the "enhanced look" component of Object Desktop. Eventually Stardock teamed up with Neil Banfield who was independently working on something similar. By combining knowledge and technology, WindowBlinds took off and now has over 2000 skins. You can find out more at http://www.windowblinds.net
Winamp has also seen its popularity grow. Originally a shareware program, it was bought out by AOL for millions of dollars. It has grown so popular as an MP3 player that even with Microsoft's efforts to dominate the media playing market, Winamp is still able to hold its own. Its third generation version incorporates very flexible skinning that supports alpha blending. You can find out more at http://www.winamp.com
WPlay, on the other hand, doesn't seem to have survived. It was a $10 shareware program that had to compete against free programs from much larger providers. It had some great skinning technology that was arguably ahead of its time. But with so many MP3 players, it was inevitable that some wouldn't make it.
So there you have it. A time machine trip back 4 years ago to the dawn of modern skinning. Back then, people didn't use graphics packages. We made skins using punch cards and each skin had only 4 colors of course... how things have changed!