As a complete NOOB, I'd like to chime in here. 

I don't intend to ask a bunch of the same old questions, but I'm sure I will.  If answers to those are hard to find, I'll either get lazy or frustrated with the search.  Then I'll feel like I'm stuck and need to ask something.  Documentation is a better way to ward off the pesky noobs than moderators, for reasons already stated. 

I'll use my situation as an example.  I'm at a decision point on my car, and will either start making simple modifications and learn to tune accordingly, stick with what I've got, or pay someone to tune it.  I'm interested in tuning myself, and would like to learn to do so.  However, I need a running car; preferably one that runs as well as the $500 OTS tune runs it, but accounting for the few small changes I'm making mechanically as I reinstall my engine.  I have little to no hope of becoming a tuner, by anyone's definition, in the next week.  I'm hoping to get my bench flash setup going (thanks to Matt Danger's blog and contributions by others), and find something to flash onto a spare ECU and get on the road.  I will have no clue whether that tune was well made, or how it was done, until I understand more of the process.  Once things are up and running, I'll have a much better ability to peruse the maps, look at the data, and learn the ins and outs. 

I've been in organizations before in which people invest really heavy amounts of time and energy building something; SAE racing teams, specifically.  In the end some of the people are happy to pass the knowledge on; knowing they did some good and improved themselves in doing so.  Others, however, are possessive of the information and think it unfair that someone can benefit from it without putting in tons of the exact same effort just to end up in the exact same spot.  It's silly, in a way, because they don't realize they themselves only got as far as they did because they didn't have to re-invent the wheel, the ECU, or Tuner Pro.  Pass on all the knowledge you can, document everything as well as you reasonably can, and watch it grow long after you have done your bit.  Don't make people needlessly reinvent your work out of selfishness.  Don't expect people to climb the same mountain just because you did.  If that happens, then only one mountain ever gets climbed. 

I look forward to working alongside you folks and figuring out what all of this is about.  I see this project following along the same lines as the DIY EFI project did.  It sarted because some clever folks didn't feel like paying for OTS ECU hardware like Haltech and the more expensive ones.  They realized the hardware only needed a few simple things to work, and started making ECU's.  They documented things well enough that someone who can handle it could get an ECU built.  Over the years a few people took that technology and made it even more accessible. MegaSquirt and VEMS resulted; both pretty huge improvements over the OTS stuff in terms of flexibility, tunability, and allowing for creativity.  This is the next step; using even less expensive technology and hardware (stock ECU's and hardware) and allowing a little of the same flexibility and tunability.  Every Noob who buys a basic megasquirt board and becomes proficient with it shouldn't feel bad he didn't start on the DIYEFI boards in 2000 and make his own board; neither should today's noobs here be made to struggle needlessly when they could be trained to advance the art instead of repeating it. 

The "hack files" are commented assembly code, someone has disassembled the machine code to assembly code and worked out what it does.
If you understand how the code works you can find the map locations, alternatively if you know the likely format of the map you're interested in then you could find it by manually looking through the file in a hex editor or comparing against known files.

This disassembly seems like it should be illegal to me.  I am no patent lawyer (yet) but this appears to me to be a form of stealing...

While I'm sure that legalities of reverse engineering code could be argued, the issue here is that bosch hasn't once asserted a right over the intellectual property AFAIK. As such, this is a moot point. In the event bosch DID want to go after tuners, I can assure you it would be the commercial entities that would be targeted. We're talking about semantics here.

Honestly, the only time I think Bosch would have issue with any modification of their code would be if someone would come along, take a sotck ME ECU, add LC, NLS, etc... and then rebrand the ECU as "Nyet's Super duper ECU" for instance.

Exactly-because lets face it, what we do doesn't have any effect on them AT ALL.

Sorry, let me clerify, disassembling, manipulating and reselling for profit seems like it should be illegal. Not the disassembling for personal use.

Not always true. I bought a physical second ecu from a tuner with a tuned file. I think your are not viewin the code as property developed by Bosch. You are viewing a tune as a service when i am viewing it is a product.