From what i've seen and my own experience (i work as an apprentice technician at a ford dealer). The mid 90's 3.8L's are crap. They blow head gaskets quite often (ford has revised their torque specifications for the heads several times) and the older 3.8L's in general signify more than 50% of the engines we replace. A guy i work with replaced three 3.8L engines this last week alone. Another thing that sucks is that if you blow a head gasket pretty bad it will cut down on the engine life in general because the coolant will wash down the cylinders (wash off the oil) which leads to scored cylinders and worn rings and can also cause rust before start up and score the cylinder walls. Engines that blow head gaskets usually don't live a whole lot longer after because of that, although if they're caught early the damage may be minimal, but that's not usually the case.
The new 3.8L's are probably much better as they have different heads/intake manifold, etc. etc. and i haven't seen any '99+ 3.8L's come in yet for engines, although it may take a couple more years for people to really get mileage on them.
This is of course, just my opinion and maybe someone will tell you different, but there are some that i've seen go 150k plus miles without so much as a single problem. I guess it's a crap-shoot as to what you get.
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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