I was looking at older/newer models when I purchased my LX. Basically, it came down to the fact that I had many needs such that a 99 wouldn't suffice. I do towing so I wanted the 5-speed tranny and I'm really glad I made that particular decision. I like to offroad so I wanted the stronger front diff and don't see any need to get lockers, at least not for the front and ATRAC works really well. Also, I use it as a DD and CO roads, especially I-70 can get pretty bad in the winter so I needed the ATRAC. All things considered, I am very happy with my 2003 even though it was at the higher end of my budget range.
It all depends on what you are going to use the truck for.
I have owned my 99 for more than 10 years now, and I can echo what others have said. These trucks are rock solid. This is the most reliable vehicle I have ever owned. I still use it as our primary long trip vehicle 3-4 times per year. At 170k it is still as solid as it was when I bought it back in 2002. My only issues have been the starter ( I wrote the DIY starter contacts thread back in 2003- cant believe that much time has gone by!), antenna mast, parking brake, front shocks, hood and rear hatch struts, and of course timing belt replacement done twice. That and getting rear ended on the interstate outside of Chicago by a Jetta. The Jetta was totaled, and I drove the rig 500 miles back to my house. Love this thing!
My family, including my wife, thought I was crazy to sell my 2006 4-Runner and purchase a 99 LC with only 82k miles. That was over a year ago and they all see the light now!