When you subscribe to Genii you get access to every issue ever printed, that's like 70 or 80 years worth of the greatest magic magazine ever published. Richard Kaufman has done a tremendous job reviving it since he bought it 15 years ago or so. So, Genii is hands down my favorite.
In second place is Stan Allan's Magic magazine, I have every edition since it's inception in 1991. It takes up the entire corner of a room.
Here is a list of magic magazines I have on CD that I've collected over the past few years. Some, like the Magic Wand and Sphinx lasted over 40 years, each and every issue is on these CDs. It's an amazing collection and it should take me most of my retirement to read (I calculated about 8 to 10 years to read everything).
-Tops Magazine (publisher Abbotts)
-New Tops Magazine (publisher Abbotts)
-The New Phoenix
-The New JINX
-Magic Mag (70s-80's version, has nothing to do with the current version)
-Chap's Scrapbook (paper version & CD version)
One poster mentioned the Magic Arts Journal. I have the paper version but I believe it's now out on CD.
I'm not sure if L&L publishing has put Harry Lorayne's Apocalypse out on CD yet, the 4 HUGE books of the individual issues. I fooled around and put off buying them and now it's too late. Unless that is they are, or ever will be put on CD.
I, too, fooled around with Apocalypse. I see them on eBay periodically and always consider buying them, but still haven't. I'd imagine the bound volumes will be back in print one day, but I'd guess never on a CD for those.
How is Chap's? I've never read any of it.