No major problems so far, with the exception of:
Leaky rear main seal.
Clutch cable adjusting nut won't stay in place very long.
Great little truck, very cheap to maintain and own. 35 mpg on average.
Don't expect the same mileage from the automatic version though, as I'm told it's somewhat less.
The seats are supportive, but not great for long trips, but neither is the Jeep for instance, another vehicle in its class.
The stock radio has some neat features, but is underpowered, and the speakers blew when I turned it up.
A great little truck at a great price these days. These things are so fun to drive as well!
I've owned a '95 Geo Tracker for five years now, and aside from a bad drivers door hinge and an odometer that stuck at 39,099 miles only routine maintenance has been done. Although it's an automatic with California emission control, it's got good low-end torque and 25/29 city-highway in the hills where I live. The only complaints I have are 1. No 4 speed transmission 2. No limited slip differential. It gets pretty hairy on ice and wet roads even in 4WD. All in all, I'm very happy with her at 90,000 miles.