Once upon a time WinCustomize's stated policy was that it would only contain the most popular apps as sections. Sections that weren't popular would be removed.
Over time, common sense grew and we realized that you can't really do that -- have a section and then remove it. What about the hard work of skin authors and such who took the time to submit something?
So we took a different route - we only would DISPLAY the most popular sections and the others would be dsiplayed by clicking on the header bar ("library") so that you can get to the other sections.
So, if you were in our shoes and had to pick say 15 sections to have on a skin site - ANY 15 sections (whether we have them here or not) what would they be with the criteria based on POPULARITY (i.e. no breaks for a "unique" freeware app please).
Where popularity is determined by a combination (pick your own way of weighting the factors in this combo):
1) Users using the program
2) Activity of skin authors
3) Legitimacy (i.e. app needs to be actively developed and developer of app must publicly approve skins being made with its format).
4) Uniqueness (should matter some, i.e. how many skinnable MP3 players should a site have?)
Here's what I'd pick to get things started:
1) Wallpapers
2) Windows Media Player
3) WinAmp
4) WindowBlinds
5) ICQ Plus
6) NeXTStart
7) Coolplayer*
8) Dashboard*
9) DesktopX
10) WinStyles
11) IconPackager
12) ObjectBar
13) Litestep
14) LogonStudio
15) CursorXP
Others that are right up there:
a) Trillian

Talisman
c) Hoverdesk
d) Screenshots
* WinCustomize is the official skin site for Dashboard and Skinplayer so they will always be part of any top 15 list.
Stardock apps that aren't listed:
1) PocketBlinds. Just isn't getting enough skinning support, has been a release candidate for a long time.
2) WebBlinds.
3) SkinStudio widgets
Other possibilities:
Beatnik (we have a section for this but lack of activity took it from the default home page choices)
SkinMem
Quick Notes
Yahoo Messenger
BTW, you can select which sections to display from your settings. So you can have as many or few that you want.