I had a 99 Grand Cherokee for about 5 months in 2005, and the following went wrong:
-It would cut off when shifting into reverse randomly
-Air conditioner stopped working, never could diagnose it
-Brake calipers nearly caught on fire after a very brief trip off-road
-Transfer case sounded like it was falling apart when shifting into 4LO
However: the creature comforts that actually did function were awesome and the power was amazing. Once 4LO was engaged, it felt like you could hook up to anything and pull it anywhere.
My dad has owned a Jeep Grand Cherokee and the front end literally almost vibrated itself to pieces. My in-laws just bought an 02 Grand Cherokee and they're already having electrical issues. Family friends have two Grand Cherokees: a 99 and a 98, and the 98 cuts off at stoplights while the 99 has random electrical issues. Another one of my good friends has a 98 Cherokee and has already replaced a radiator, various coolant lines, and currently has several electrical issues.
Keep in mine: all of the above mentioned Jeeps have 30-60k less miles than my 4Runner WHEN I BOUGHT IT. So even with the rough suspension, it was miles and miles above the Jeeps.
I can say definitively that if you even have a hint of desire to buy a 4Runner, do it. The Jeeps are cheap and feature-packed, which makes them seem to be a good deal, but while we are replacing suspension bushings and finding proper tire balance shops, Jeep owners are replacing transmissions, rear ends, and fixing countless electrical issues.
Chrysler is so full of fail, it's ridiculous.