Alcohol is one of the best (I'd actually say: the best) Software for creating virtual CD images that are as close as possible to the actual medium. GJ, however, follows a different approach: When first starting your game with GJ, it tries to find out which parts the medium are actually read out. After this first start, GJ creates a (in most cases) very small emulation image, containing only those parts of the CD that are relevant (i. e. must be read by the copy protection or are not located on the harddisk).
So GJ is more suitable for games and creates much smaller emulations that a true 1 to 1 virtualizer such as Alcohol does. Alcohol, on the other hand, can emulate almost any type of media, including audio CDs, video DVDs and more. So you can say that Alcohol and similar tools are meant for copying whole media to the hard disk, to have the data on them more closely to your fingertips, whereas GJ's task is to make Games "CD free". If you only need the latter, than GJ would be the better choice.
