Attempt at P.A.P. DeSmuME

Manual about icons.
If the application also uses multiple icons (as detailed above), these additional icons are named as appicon1.ico (appicon1_16.png and appicon1_32.png), appicon2.ico, etc. The numbers correspond to Start1, Start2, etc within the Control section.

So, what I did (and what hopefully solves your problem): copy appicon.ico three times and rename them to appicon1.ico, appicon2.ico and appicon3.ico.
Recompile the launcher (not sure if needed, can't go wrong doing so).
Refresh icons in PAP (right click, refresh icons or something =p)

Hope this helps!

Looking through your files I found a lot of issues. I'll start with the ones I can see without actually running DeSmuME:

Icons

• You can remove the icons in AppInfo\Launcher, only the ones in AppInfo are required
• You can remove the appicon_16.ico file, you only need appicon.ico and the .png files
• Within your appicon.ico you need 16, 32 and 48 pixel versions in both 8-bit and 32-bit (so 6 icons within the file, with an optional icon at 256 pixels in 32-bit)
• Because you have a multiple executable package, you also need to create a separate copy of appicon.ico and both .png images for each item you want listed in the Platform with the following naming scheme: appicon1.ico, appicon1_16.png, appicon1_32.png, appicon2.ico, appicon2_16.png etc. for as many executables as you want listed in the Platform (three in your case) - this is why your icons aren't showing up

appinfo.ini

• You can remove the InstallType= line since nothing is being set
• Unless there is an EULA in the package you can remove EULAVersion=1
• You should mark CommercialUse=true as the GPL allows it
• The [FileTypeIcons] section won't do anything unless you have specified an [Associations] section with some file types associated
• It looks like DeSmuME is English only (can't see any language files) so you should set it to Language=English (or am I missing something?)

launcher.ini x3

• I think you are a little confused with the [FilesMove] entry in each launcher.ini. This entry makes the file on the left side (eg. settings\DeSmuME_devPortable.ini within the Data folder) move to the folder on the right side (eg. %PAL:AppDir%\DeSmuME_dev) when the app starts. I would presume that all three executables actually used desmume.ini while they are running. If that is the case you would actually want one of the following:
  To have all executables use the same settings: desmume.ini=%PAL:AppDir%\DeSmuME in all three launcher files or to have separate settings for each executable: DeSmuME\desmume.ini=%PAL:AppDir%\DeSmuME
DeSmuMEdev\desmume.ini=%PAL:AppDir%\DeSmuME
DeSmuMEnosse2\desmume.ini=%PAL:AppDir%\DeSmuME (one in each launcher.ini as appropriate).

  Either way you will run into trouble when running more than one of the components at the same time, which you may be able to prevent from happening with some custom code (not my field, so someone else will have to give you a hand there).

• You aren't updating any of the paths in desmume.ini, so portability will break as soon as you move to a computer that assigns a different drive letter. Have a look at the [FileWriteN] section of the Launcher docs, and also take a look at an official app that updates paths like Pencil Project Portable (FileWrite 4, 5, 6 are the ones in Pencil that would be of use to you).

Other

• You've got the name of the DefaultData folder as DeafaultData - it won't be used like this
• If you are supplying desmume.ini in the DefaultData folder, it shouldn't also be in App/DeSmuME
• You have added AviFiles, Cheats and Lua folders to DefaultData but never do anything with them. Should they be moved to/from %PAL:AppDir%\DeSmuME with [DirectoriesMove]?
• Should the Roms folder also be in Data (and DefaultData if the app can't create it itself)?
• Your desmume.ini in DefaultData has paths from you running the app (d:\My Documents\Documents\Roms\* and d:\My Documents\PortableApps\desmume\*). These will break portability. If they don't need to be set remove the lines, or if they do need to be set, set them as eg. DEFAULTROMSDIR, DEFAULTBATTERYDIR etc. and add a [FileWriteN] to the launcher.ini files for each to replace it with eg. %PAL:DataDir%\Roms. Have a look at LAN Messenger Portable's [FileWrite6] and compare with the App\DefaultData\Roaming\LAN Messenger.ini file for an example of this in an official app.

Sorry to overload you with stuff there, but if you need any help or clarification let us know.