Here is a link to a write-up by bismic on the differences between model years of the 6.0. This has been a point of contention for a while and there are good and bad 6.0s in all years of it. My '05 has been flawless so far but it is all stock with no mods at all. It has been completely reliable and I have only had to replace the batteries.
http://www.ford-trucks.com/forums/84...del-years.html
When you get a chance, go to bismic's profile page and search all threads by bismic. Absolutely some of the best information out there on the 6.0 and common problems and solutions.
All in all, most agree that most of the bugs had been worked out by the '06-'07 runs of the 6.0. There are a lot that also include the '05 in that. Then again, there are a lot of '03 and '04 owners that haven't had the problems that many have reported. One thing to keep in mind also is that you will read a lot of horror stories on forums like these mainly because their owners are experiencing problems and have sought solutions. What you don't see as often are those that have had no problems. This is generally because owners that aren't having problems aren't seeking solutions.
One of the most important things to do if you find a truck you are thinking about buying is to get an OASIS report. This can be done on this site here:
http://www.ford-trucks.com/forums/78...vin-tools.html
After you receive the OASIS, you can look at it and get on here to ask questions about it. Just don't post the actual report as it is copyrighted by Ford. The OASIS can give you a lot of insight into the vehicle's history and warranty repairs made to it. A Carfax is good as well. Just remember though, that work not performed at a dealership will not appear on the OASIS. Likewise, there is a possibility that work could have been done on a vehicle and it didn't get reported to Carfax.