I really love to hear the voice of the Analytics experts about this.
Here my two cents:
a) The easy way: different GA for each magazine. Segmentation is perfect and you can collect data from different domains and subdomains. Piece of cake.
b) The hard nice way: Same GA for every magazine to let you have a global overview of the service... but it a nightmare.
About a) not much to say. Create GAs, assign to the magazines and ejoy.
About b) you will need to create profiles with filters.
WARNING: BTW, google recommends to keep a clean profile (Master) with all the collected data without any filter, just in case you delete a profile and the associated info.
I was dealing with it long time ago and I arrived to the conclusion that the easy way was working with the apache logs and awstats.
Any way, my case was a little bit more wired because I allow multiple domains for the same magazine (robots.txt excluded to avoid penalties) for instance it all belongs and redirects to the same magazine:
When I played with Analytics, my idea was mixing it all... and offer global numbers (to the magazines service) and unified numbers (to the magazine's editors), but Analytics didn't think this should be a nice idea.
As I said, waiting Analytics to get more light about this.