First Generation Pneumatics - 1984 - 1989

The first generator Lego Technic pneumatics parts were released in 1984 and formed the Universal Set (set 8040). There was 6 different parts - pump, switch, distribution block, t-piece, short and long cylinder. This generation of cylinder only had one inlet on the cylinder, so either worked on pressure or vacuum.
The cylinder is about 6 studs long and extends by 4 studs. There was also an 8 stud long cylinder offering an extension by 6 studs. Both work on pressure to go up, and a vacuum to go down. The vacuum was created by the distribution block by some one way valves. This required some very special linking of the tubes together.
Advantages - With only one pipe running to the cylinder this allowed easy remote installation of the cylinder.
Disadvantages - Relied on a vacuum to retract the rod which didn't provide much power. Complicated tube layout due to the need to separate pressure and vacuum lines running to the valve. Very difficult to position cylinder in anything but fully in or out. Rod extension and retraction can be jerky and sudden.
Second Generation Pneumatics - 1984 - 2007

The second generation came along in 1989 and replaced the pump, cylinder and did away with the valve block. They also redesigned the T-piece, but kept the same part number. The cylinders now had 2 valves on them allowing both in and out to pork on pressure rather than a vacuum.
The first model they appeared in was the Backhoe Grader (set 8862) which contained 3 of the new cylinders.
Again the cylinder was a same size - 6 studs high covering a 4 stud extension. This time there was an extra air inlet at the top of the cylinder and this allowed in to work on pressure to extend and pressure to extract. This proves far more force when trying to retract.
In 1992 Lego introduced a new smaller pump that allowed it to be motorised along with a new smaller cylinder. This cylinder is 4 studs long and extends by 2 studs. The pump was easily attached to a motor via gears providing a way to build a compact compressor.
In 1997 an air tank was introduced - this comes in handy when used as part of a Lego Technic Compressor.
The last Lego Technic set with pneumatics was the Tow Truck - set 8285
Advantages - Pressure to extend and retract the rod provides great power. Fairly easy remote installation of cylinder from pump and switch. Easy to build remote compressor. New small cylinder allowed smaller mechanisms such as grabs.
Disadvantages - Very difficult to position cylinder in anything but fully in or out. If it is possible to position rod half way it moves easily with any degree of force on the rod. Requires 2 tubes to remotely install the cylinder. Rod extension and retraction can be jerky and sudden.
Linear Actuator - 2008 -

In 2008 Lego introduced the new Lego Technic Linear Actuator. It was first included in the Technic Excavator (set 8294) and shortly afterwards the Telescopic Handler (set 8295)
The actuator is about 8 studs long and can extend about 5 studs distance. The linear actuator works by an internal screw mechanism powered by an axle socket at the end of the actuator. Within the actuator there's an internal clutch to prevent it being damaged. To extend the actuator the axle socket needs to be turned about 25 complete turns.
2 Brackets are available for mounting the actuator. This allows various gears to be mounted to power it. At 25 turns it makes long work if the actuator has to be extended fully or retracted manually.
There's an excellent article over at TechnicBricks with various mounting and gearing options. http://technicbricks.blogspot.com/2008/08/tbs-techreview-05-technic-pf-linear.html
Advantages - Cylinder rod can be positioned in any position from fully in or out. Once in that position it stays there. Easy to add a motor to the cylinder. Rod extension and retraction is smooth.
Disadvantages - Really needs a motor to run due to it requiring 25 turns to extend or retract. Remote installation is possible but requires complicated gears and rods.
So which is the best?
A lot depends on what you want to use them for. The second generation pneumatics seem to offer the most push and pull power, whilst the actuators give infinite variation. The pneumatics are either in or out as it's near impossible to provide enough air pressure to keep them midway. The first generation of Pneumatics were innovative but reasonably limited.
The Linear Actuators would be greatly enhanced if Lego were to introduce a new small geared motor. We already have a Medium and XL Motor so it's possible a small motor is in the pipeline.