Just to get everyone ready for the cyclowiz upgrade I figured I would show you the whole procedure step by step that way you aren't lost when you get it. You could have always just followed the onscreen directions when you got the chip but this way you are prepared for whats to come. Follow these and you will have a perfect flash

The first step is optional, You can turn off wiiconnect24 just to make the last step easy. Turning off wiconnect24 automatically turns your system all the way off without standby mode. If you choose not to turn off wiiconnect24 then make sure you hold the power button down at the end of the flash so that you get the red led.
Remember that if you're burning your upgrade disc to dvd+r then you should set the booktype to dvd-rom. After the upgrade though you won't have to do this anymore. Once you put your disc into your wii your system should read it as a gamecube disc

If it doesn't then you burned your image wrong. If it did then choose the gamecube icon and then start. The first screen you see is the welcome screen
The first step here is to eject the disc. Take it all the way out of the system, you won't need it anymore. After ejecting the disc you will see this screen
Here is where you test your switch to make sure its installed properly for the upgrade. Simply turn your switch on and then press reset. After you hit reset you will see

This will let you know what to do incase your test fails. Once you know what to do just incase then flip the switch off. After a second or two you will see this screen if your test is successful

Do what the screen says and turn the switch on and hit reset. The next screen you will see a flash status bar, this is the first time it will appear but it will not go all the way. Instead it will go 1/4th the way. This is completely normal.
The bar will go about here and then jump to the next screen
The next screen will tell you to turn your switch off and then back on before hitting reset. Please make sure you follow the directions here. Turn the switch off, wait a second and then turn it back on

After doing so you will get the final flash. DO NOT TURN YOUR SYSTEM OFF!. Wait until the flash process is complete even if it goes slow.

After the flash is done you will get the following screen

This will let you know to turn your switch off and then hit reset unless it fails during verifying the newly flashed firmware. If that happens you will be directed back to step one. If the flash verifies successfully you will see the following screen

Remember that if you did not turn your wiiconnect24 off you must power your wii completely down before the chip will work. After turning your wii on then you can reenable wiiconnect24 if it was off and then you are ready to try your nonworking games.
EDIT: Since this has been posted the upgrader has been released for non d2b systems but now the upgrader is hybrid and can be downloaded from here
CycloWiz-3.0B-NTSC-USA
CycloWiz-3.0B-NTSC-JAP
CycloWiz-3.0B-PAL
Here is a gcos compatible with cyclowiz which gets all your old cobra multigame discs working
Gcos Compatible with Cyclowiz
Get the one that matches the region of your wii