I can't imagine mechanical fans working on anything but longitudinally mounted engines, which are really only common to trucks, SUV's, sports cars, and classic cars. They are probably still being used because they are cheap, and with a fluid clutch can still be effective/efficient.
Thats what I have, a front engined rear wheel drive truck..
they use em on just about every rwd truck out there..
Headers:
Any aftermarket exhaust is going to be interested in high-hp, which is not useful for hypermiling. Headers that are "tuned" to shift the torque band into lower rpm's would be useful, but they would probably have to be custom made and mated to higher gearing to be useful.
so a direct fitment mite not be the way to roll then?
Freeflow Exhaust:
I don't see much of a benefit as under hypermiling conditions the exhaust shouldn't be much of a constriction.
I can see it from that point of view, but what about in reguards to FE and low end torque?
Electrical --> Mechanical Fan:
Beneficial, especially if the fan is not clutched (unlikely). I've seen people switch from clutched fans to electric fans and record a mpg/hp improvement, but I bet the improvement is less than moving from an unclutched fan.
I'm not sure if its clutched or not..
but I'll find out.. 
Aluminum Flywheel:
I'd like to know.
I'd assume lowering reciprocating mass would lower friction/energy consumed, but it kills the idle and makes it easier to stall. Some first had testing would be nice...
reciprocating? maybe rotational.. thats a new one to me..
google a "reciprocating saw" and compaire that to what a flywheel does.. 
In terms of street/driveability, takes a little bit to get used to it ,
but it was very daily drivable.. made a great deal of difference in acceleration and hp difference in a race vehicle i had, not sure about FE goals tho
Underdrive Pulley:
I would expect a marginal improvement in mileage, but I have no idea of the impact on the cooling or oil pump. An underpullied alternator will probably make up the speed difference by increasing field current (i.e. no MPG gain). Removing items from the circuit (alternator delete, electric coolant pump, etc.) will see bigger gains.
alternator delete? 
how far would ya get till you kill the battery then the ecu looses proper voltage and your DOA.. I donno about that.
High-Output Alternator:
Not too sure on this. I don't know whether a larger alternator could charge a battery faster than one smaller...which is the only area I could see a decrease in engine load.
Its something I want to do for stereo equipment and having an onboard compressor setup..
- LostCause