Definitely take it -135 - it has nothing to do with which part you can fly under, and when you get your ATP, it's just an ATP, not an ATP (135) or ATP (121). Even when applying to airlines, those that require the ATP written require just that, not the -121 written.
The advantages of the -135 written are that the rules are easier (though you'll find later on that most of -121 isn't much different than -135), and you're probably still somewhat familiar with -135 from the commercial written. The biggest advantage, though, is that the weight & balance, performance, and flight planning problems are much easier when you're doing the numbers for a B1900 than a B747 - if nothing else, no MACH to TAS conversions! Your chances if getting a good score are better, and while it's not the most important thing, a good score is nice to hand to an interviewer - you want every competitive advantage you can get.
Of course, once you get your ATP, they won't see your score anyway...
The FAA only gives two versions of the written as a courtesy to those pilots that are already flying under (and hopefully familiar with) the rules of one part or the other - so if you're not a -121 pilot I would avoid the -121 written.
I'm not familiar with the Jepp software, but I would reccomend the Gleim highly. I used ASA a couple of years back for the FE written, and it was OK, but whenI had to renew it I downloaded the demos from both ASA and Gleim and ended up going with Gleim. Whichever you use, try to familiarize yourself with as much of the base material as you can before you start working on prepping for the written itself - you'll do better, and you might actually end up knowing what you're talking about ;o).
As for American Eagle, the best we've heard for recalls is the summer, though rumors are circulating that we could start bringing a few back before then. No one is getting their hopes up yet.
The airlines that are hiring, at least some in the near future, seem to be the ones associated with United and Delta - look at ASA, ACA, Comair, and SkyWest. There are others, but this group seems to be in the best position right now. Unfortunately, the market has become brutally competititve, but then, by the time you start getting in the window things may have snapped back.
And follow what's on this board. It's not always accurate (consider the sources!), but over time you ought to get a good picture of what's going on.
Good luck.
