Those are icons of emulators which are archived in the OPK files I believe.
So you would have to unpack them modify the icon and repack them.
What Aeter said. If you wanna change the icons for emulators/games, you need to uncompress them and then repack them with squashfs.
For example, here's how you repack a directory "opk" into an opk file.
mksquashfs ./opk oswan.opk -all-root -noappend -no-exports -no-xattrs
As for getting the binary from the OPK, just rename it to .zip and open it with File-Roller (Linux) or 7zip on Windows.
As for the system icons though, they don't come from OPK files though.