For anyone else on Windows wondering why there wasn't a compatible executable in the tnes-converter zip, this post (
http://gbatemp.net/threads/gbc-vc-generator.371819/page-7#post-5148680) contains an attachment containing a variety of tools, including a Windows-compatible version of the tnes converter!
What you need from the vcpkg zip is the cygwin1.dll and tnes.exe. Extract them from the zip in their own folder if you want; I recommend doing so because it'll make it easier and more organized when you have to convert the NES games later. Also, since you will be using a command-line to convert the games, I also recommend renaming the games so that there are no spaces in the name (i.e. GI Joe.nes renamed to either GiJoe.nes or GI_Joe.nes). Once you are ready to convert your NES games, open up a command window in the same folder where tnes.exe and cygwin1.dll are; an easy way to do this is hold Shift and right-click anywhere in the folder. You should see an "Open Command Window Here" prompt in the context window. Once you open the command window, type "tnes inputrom.nes outputrom.nes" (without the quotes around it) with "inputrom" being the game you want to convert, and "outputrom" being the name of the converted rom to properly convert your NES games to the format needed for the VC. Once that's done, put the game(s) into the rom folder of the romfs, and follow the rest of the steps in the first post to recompile your new romfs for the VC you wish to inject into.
For the record, I've successfully injected into Legend of Zelda, and everything seems to be running fine