New changes are complete. The new
d2x page replaces IOS249. Also, update your Cfg to v69d.
The most important thing about this new cIOS is it makes pretty much all the games that didn't work... work. Metroid Prime Trilogy, Sam and Max, Smash Bros. Virtual Console stuff and other things should all work fine now.
Us the tutorials there to install the Homebrew Channel, d2x and Configurable USB Loader. It will help you rip the games to the hard drive (check the notes on the Cfg page about how to get ISOs for Dolphin). There's also another app which might rip a little faster, but I can't remember the name right now (I think it's CleanRip or SmartRip).