OK, so my 2 cents on this resurrected but stickied thread.
Appearance and amenities:
The big appearance difference is the old school rectangular headlights on an fj62 vs the even older school fj60 round head lights. It's a matter of taste, but functionally speaking, 4 headlights are better than two. Amenities wise, the power windows and door locks, the push button 4 wheel drive, and the power antenna on the fj62 can be problematic. Once you get those fixed, they are great. Why would you not want to be able to lock/unlock all the doors and roll up and down all the windows while sitting in the drivers seat? Being able to engage the 4 wheel drive at the push of a button is great, and with the antenna down, it won't get broken off. The fj62 definitley has the egde as far as convenience goes. All those conveniences can be problematic, but they can all be fixed. There are threads right here on MUD to be able to permanently and inexpensively fix every one of these power options. Once they are fixed the right way, they will be good for another 20 years.
Mechanical:
Due to the single fact that the 3FE engine in an fj62 has Electronic Fuel Injection means it is better than the 2F engine found in the fj60. Yes, the 2F may have a little more low end grunt, but there is a reason you see quite a few 2F engines being swapped out for 3FEs on older Cruisers. The EFI is a big improvement over the carburetor. That is the reason all cars made for the last 20 years have EFI. For someone that has become an expert on carbureted engines, the 2F may be a better choice than the 3FE, but I think for most, an EFI engine is a better choice. Ten years from now, it may be real tough to find parts and expertise for a carbureted engine.
Many feel that the A440F automatic transmission in the fj62 is the achilles heel of the beast. The fact that most of these transmissions go 200K+ miles says otherwise. The problem is, many of us are taking possession of these rigs right about the time that the transmission wears out, so our first big hurdle is the tranny. The A440F can be replaced with a rebuilt/upgraded one from Australia and the achilles heel is now a point of strength. Yes, the Australian tranny will cost about $3K (or more depending on the rates of currency exchange), but so will swapping in a 5 speed manual, and the engine will be revving higher going down the freeway with the 5 speed than with the auto. The 5 speed is geared lower than the auto, which is the reason the 3FE feels like it gets a power boost with the 5 speed. The good news is that the issues with the auto transmission can be delt with permanently by either replacing it with the Australian (Wholesale Automatics) or by doing the 5 speed conversion--depending on your personal taste. Don't see too many auto tranny options for an fj60. So once again, the fj62 wins this round. Remember, this is my 2 cents. You can have yours next.
Conclusion:
Both the fj60 and fj62 have their proponents. Some just can't stand the rectangular headlights. This is OK. If we were all the same, it would be a boring world. But, if you are looking to buy a 60 or a 62, you should realize that even if you are starting with a clean and minimal rust rig, you are going to be looking at several thousand dollars after the purchase price before you have an updated and reliable, driveable rig. It takes a lot of work to overcome years of deferred maintenance. Then, if you want to add off road equipment, you can tack on another 3 or 4 thousand. But, I would rather spend $10K on one of these and have a rig that will take me another 100K miles than spend $30K on a new one that will take me 100K miles or so. The $20K difference in price will more than pay for the difference in gas, not to mention the difference in taxes and insurance.
So, if you are standing at the cross roads, pick the fj62. Mechanically and amenities wise, it is a more modern vehicle. You can fix all the problems with a little time and money. If you don't have the time, or don't want to spend the money, don't buy one at all. Go buy a new rig, and 10 years from now, I will still be driving my then 30 year old cruiser, and you will be making payments on yet another new vehicle.