Well got the word this afternoon that they are ordering me a new engine and all the related parts for my 8, and its a 6 speed not an automatic. I've spoken with the dealership managers and corporate Mazda and no one really has any idea what is wrong with it. So I guess replacing the engine this time is the solution, rather than the dang spark plugs and coils again. It has been in the shop 4 times now (2 months total time literally at the shop) over the last 3 months with engine issues, very rough idle, 'woofing' sounds, the works. At least they are doing something about this time, though really I hate that it has taken all this trouble and time. Anything I should be worried about?

Also I heard that putting a new engine in a car kills the resale value buy 50% of blue book. That just doesn't seem right. Anyone know if this is true?

Dude I would not be worried at all. First I'm sure they will take extra care in the install. Second, I'm not sure how long you have had your car. But with a new engine it will be like having a new car all over again. (I wish my engine would blow before the warranty was up so I can get a new engine).
Sit back, relax and wait for the new engine. Once installed follow proper break in procedures as noted in racing beat.com, care for the baby with frequent oil changes and occassional hard driving and enjoy the fun

Sorry to hear about the car but at least they are changing the engine. You will have ywear with the new engine. As far as resale I don't think that it would hurt but I'm not sure. Most places wouldn't know that you even changed the engine and if they did Mazda did the warrenty work just keep all the paper work. I wish Mazda would fix the dead spot in rpm range I love ethe car but that gets a little annoying.