Magic Engine is the easiest emulator to operate, but don't be a thief; buy the full version or deal with the time limit. Use something like daemon tools to mount the iso (use google to learn more about disc image emulators), then start M.E., press escape to bring up its menu (if it doesn't appear automatically), then click on file - boot cd - virtual drive with mounted iso. To avoid compatibility problems with M.E.'s built-in system card, use google to find rom images of the real system cards and save 'em in the same folder as M.E.
I disagree. Magic Engine USED to be the best ever.
However....
Ootake is far easier to operate, especially if you are used to a Windows environment. Everything you could possibly want to fiddle with is right up top in nicely organized menus.
Changing settings is easier, there are more features in general, and it runs better. Also, it is free and updated pretty regularly it seems. It even runs Super Grafx games.
http://www.ouma.jp/ootake/If you place any ROMs (HuCard games) in the install folder of the Ootake directory (Usually: C:/Program Files/Ootake/Install), thats the default rom directory so loading games is a snap.
You can set System Card 3.0 easily in the menu also. The menus are all simple Windows style drop downs. Just press CD-ROM and then "Set System Card Image" and pick System Card 3.0. I can't post it here, but you should be able to find the rom no problem.
I suggest you try Ootake out. I use it for PCE development testing and so far things have been near perfect to the real hardware. It will run real CD games if you set the CD-ROM drive letter to your physical CD-ROM drive (again, in the CD-ROM menu). Or you can set it to a virtual CD ROM drive like a Daemon Tools or PowerISO drive. With virtual drives, you can mount downloaded ISO or bin/cue stuff and play them if you set the CD-ROM drive letter to the virtual drive.
Give it a try and let me know if you have any problems.