GRoche,
Why didn't you ask an easy question like 5 speed vs automatic or 2wd vs 4wd!
Seriously, I have one of each so I'll chime in. I suppose a lot has to do with what you plan to do with the truck. Mine see mostly commuting duty with the occasional light slide-in or towing my 66 plymouth, so I would classify my use as light. Both trucks are stock in the HP department as well. Seat of the pants I don't notice much power difference between the two - both are more then adequate for my use. The 4x4 auto gets almost the exact same mpg as the 2wd stick, which leads me to believe that the 12 valves are a little better in the mileage department. I haven't had any serious mechanical issues with either, so I can't comment on reliability (both good!)
The 12 valve is louder, smokes more and is generally more of a truck. It feels more solid - and thats with 1. 5 times the mileage then the 24 (93k vs 63k). Hard to compare, but my instinct is the 97 is tighter all around then the 99 and would outlast it.
That being said, the one downside - and what will likely cause me to have to part with the 97 this fall - is the truck configuration. Aside from the rare 98 quad cab short beds, you either get a regular cab long bed or a extended cab long bed. If you have a standard garage, the regular cab is probably the only 12 valve that will fit inside (a requirement for me - wife is short and doesn't want to scrape windows!) Due to the scheduled arrival of our first child, I will probably find myself upgrading to a 3rd gen quad cab in the not to distant future, but only because I need the extra cab space, not the extra valves.
Good luck on your hunt. It took me almost a year to find this one, but they are out there.
-Vic