Is there any advantage of 1 gear combination over another IF the end gear inch is the same?

The gear ratios are on a bike and the crank arm length and the rear wheel will be the same so the end result will be the same gear inches and there would be no additional leverage at the pedals due to longer crank arms.

Is there any mechanical advantage (ie leverage) of using one gear combination like a 52 front sprocket and a 13 rear cog which is a 4:1 ratio OR a 48 front sprocket and a 12 rear cog which gives the same gear ratio of 4:1
OR
Lets say I expand that and include an intermediate gear. A 32 in front a 16 cog in the middle driving a 28 sprocket and a 14 cog last which the end result is a 4:1 ratio

60 / 15 or a 44 / 11 ?

No, your final ratio is what counts. Of course putting a extra set of gears in your intermediate example would add friction to the drive train though.

No its 6 of one and half a dozen of the other!
same same..

No advantage and you will like this handy gear calculator:

http://www.sheldonbrown.com/gears/

Input the info and calculate your gears. You can print a copy for your bars if you want. It is easy to see the duplication of gear with different combinations.

Yes, but for most people it is not enough to bother about. Generally a well maintained good quality chain will transfer in the order of 90-98% of the power at the cranks to the wheel.

There is more friction losses when smaller spockets are used. Most of the extra losses result from each link needing to bend and straighten further to comply with the tighter radius of the smaller sprocket. (under tension)

(Going from memory) Once you get above 15 teeth, it gets very difficult to measure difference in power loss. So looking at that 60/15 versus 44/11, I'd expect the 60/15 to be significantly better in terms of power transfer. (possibly as high as 10%)

If you were to use an intermediate gear you could expect the losses to double (two chains and extra bearings).

Here is a link if you not convinced.
http://www.jhu.edu/news_info/news/home99...