I owned a 1996 3rd gen for almost 9 years and updated to a 2007 GX470 4 months ago.
I liked my 3rd gen a lot, and I used it to tow my boat, but at #4500 it was really pushing it for the V6 (I upgraded to Tundra brakes at least)
Reasons I chose the GX over the 4th gen 4runner (or tacoma):
All have V8
All have a 3rd row
All have side curtain airbags
All have rear Air conditioning (from the roof down)
More head room
All have air bag suspension - many here don't like it, but I do. It makes towing much simpler when the car levels itself. (The 3rd gen would squat so I put in manual inflating air bags/coil helpers)
The other day I helped a friend move, I loaded the back up and then put on a hitch cargo carrier and loaded it with another 200lbs which were cantilevered out. I started the GX, and it leveled right out.
Most components of the air bag system are $60-200 to replace. The main exception being the compressor. Yes, go to the dealer and the air system is $1200-2800 to repair/replace. Dont go to the dealer!
What I liked better about the 4th gen 4runner
meaner looks
slightly simpler
rear door opens up instead of to the side which is nice in the rain.
The reasons I chose the GX over keeping the 3rd gen
Safety features - wife and 2 little kids are important to me!
Going to put money into maintaining an aging vehicle, might as well do it to the vehicle I will drive for the next 10 years
V8 for towing - the GX has roughly 90 more HP and 110 more torque.
3rd row - we have a vehicle that we can carry friends/kids friends in
Other benefits:
WAY more comfortable
WAY quieter - I dont have to yell to talk to passengers in the back seat
Better headlights
roomier (cargo may be slightly smaller especially with the 3rd row)
roll down the windows with the key fob on a hot day
bump the key to start (dont have to hold it and crank)
The 3.4 was pretty good, but the V8 is even smoother!
Downsides to GX vs 3rd gen:
fuel "economy" neither vehicle is good, my 96 4x4 got about 16-17mpg, the GX gets 15-17 usually tending on the low-mid part of that range.
"requires" premium fuel - really up to the owner. accelerates smoother on premium, but drives fine on regular
I care about the finish/interior now! - a far cry from the indestructible cloth, and the already faded/peeling 3rd gen.
Miss my 12" sub that tucked neatly over the rear wheel well. (still have it if anyone is interested!)