For some collections you can easily use tools to decrypt the ROM files that are on the CD or DVD, but for others, like Sega Smash Pack and Sonic Mega Collection, there are no tools. I could have just downloaded the ROM files, but that seemed like cheating.
Anyway long story short eventually I learned enough about computers to get the Roms extracted by cutting them out of the computer’s ram while the collection had the game loaded. I thought someone else might be interested in doing the same thing so here’s a little guide.
In this guide I will extract Sonic the Hedgehog 2 from Sonic Mega Collection (GC)
First rip the Sonic Mega Collection (SMC) disk. Cleanrip for the wii is the easiest way to do this.
Next download and install Hxd. This program is a hex editor that also allows you to view your ram.
After that download the latest 32-Bit build of the Dolphin Gamecube emulator. It has to be the 32-Bit version, because Hxd can only view the ram of 32-Bit programs. For this task it doesn’t really matter if you get good Fps running dolphin so don’t worry about that.
Run dolphin, click GC pad to configure the controllers keys, and then tell dolphin to open your SMC iso you made with cleanrip.
Ta-Da, its Sonic Mega Collection. Oh joy.
Go to the game menu. I find the title screen to be unresponsive and have to mash the start button a ton to get through it.
Now the interesting part begins. Select Sonic the Hedgehog 2 on the menu. If you get a black window but dolphin doesn't crash don’t worry it should be OK still. Pause Dolphin so it quits eating up CPU and start HxD. You may have to run HxD as the administrator.
In HxD pick “Extras” and then “Open Ram.” and select dolphin from the choices.
Click “Search” then “Find.” Click the text and case sensitive options and search for “SEGA GENESIS” (for some games it's SEGA MEGA DRIVE) press F3 to continue searching until you get to something like this.
Now from the Sega genesis row back up 16 rows.
I find it's easiest to count by holding down the mouse button and selecting the rows as I go. Click at the very beginning of the selection after you've counted.
Look up the size of the game cartridge. Wikipedia usually says what megabit a cartridge was. For Sonic the Hedgehog 2 it's 8 megabits. HxD, being a hex editor, likes to work with hexidecimal numbers. To convert the decimal amount of megabits, in this case 8, to a hexidecimal amount of bytes you must take the number of megabits times 12500. For 8 the result is 100000.
Now you can click “Edit” and then “Select Block.” Make sure the “hex” option is set, then select length and put in the number we got in the previous step.
Now click the little paper in the top left of HxD to make a new file. Press Ctrl+v to paste the selection in to this new file. Click file and save as. Save this new file as a romname.bin file, but put something appropriate in place of romname.
There you have it. That is the rom. Now there are all kinds of amusing things that can be done with it, as you probably know if you are reading this guide.
If you want to do this to some other collection use the same basics steps. Start the game in the collection and then cut out the ROM file using HxD.
As some extra tips, if you want to do this for all the games on a collection download a save from gamefaqs so you don't have to unlock the games. Also make a save state in dolphin at the game select menu.
Please post if you've got comments, suggestions, questions, or found a mistake. Sometime I might make another guide on rom extraction if there's interest.
If I understand the large, right under my nose, 
