the 00000001.app cant be 'extracted' as its a .dol file (wii executable) not an archive. If you really want the rom your best bet is to open the 00000001.app up in a hex editor and search for it and cut it out manually. Try searching for the iNES header to show you where the rom starts (ie. search for NES in ASCII)
oh, and also most 00000001.app will now be LZ77 compressed so you will have to decompress first.
heres a little lz77 tester/extractor i made up using the wwcxtool from wwpacker, its pretty much just a .bat file packed into the .exe
http://dl.dropbox.com/u/2910362/LZ77%20tester.exe
I will try and see what i can do to make some sort of cutter to use with something like vgmtoolbox
EDIT: ok seem to have got something worked out here
http://dl.dropbox.com/u/2910362/vgmtoolbox_bin_r590a.rar
1 - decompress 00000001.app with LZ77 Tester.exe
2 - open VGMToolbox.exe
3 - Navigate to Misc. Tools>Extraction Tools>Generic>Advanced Cutter/Offset Finder
4 - In presets dropdown box select Nintendo Wii VC - NES ROMS and press 'load' button
5 - Drag your 00000001.app into the field where it says 'Drag and Drop files to search here'
6 - rom should be be cut and put in a folder
also if your NES VC happen to be Famicom Disk System i will need to edit the .xml, but thats only for JPN VC anyway.
