Most of those apps that are being done by big companies, ie: Times, or any Conde-Nast magazine are being built from scratch by programmers in-house (or contracted).
As far as I know, there is no "easy" way to get there at this stage. You have to be able to program and get the device to do what you want.

As of yet, Indy CS5 has not been integratable into the iPad. They are apparently working on it last I checked.

Well as it is, I'm creating my folios (iPad magazine apps) with the Adobe DPS package, which includes Overlay Creator, Bundler, Viewer - and a custom Indy script. I'm using a few pre-release updates of these programs, but the difference between those and the released stuff isn't that big.

I can do a lot of the stuff they've done with the Virgin Project and Times, but there are a few functions which I can't replicate. I can't believe they custom-program this stuff. There must be some program or plug-in I don't know about.

Here's a tutorial http://bit.ly/dJMX1m

Woohoo! I found out that Virgin Project was made with WoodWing - not Adobe DPS. Apparently, WoodWing is a lot more functional than Adobe.

So it looks like the specific functions I wanted to replicate from them just can't be done with the Overlay Creator. Looks like you were right about the Times' infographics, Audentia - they're made by a company called Applied Works who reveal nothing about how they do it, except that they have "programmers" working on the project.

If any of you are considering buying software for creating iPad magazines - it's worth checking out WoodWing. I can't use it at work, because we're tied in with the Adobe pre-release program - but I'll see if I can get my hands on some WoodWing anyway.