Essentially we need something to evaluate scarce resources that are currently measured in infinite resources (dollars). This concept has a rich history...

Unfortunately, concepts like the X theory of value - for example Henry George's land theory of value - also have a rich history of deep problems, inasmuch as individual commodities of whatever sort, even patently finite ones like land or oil, pose individual and idiosyncratic problems. Among other things, these X theories neglect substitution. The unavailability of perfect substitution is not the same as the unavailability of any substitution, a point I think some hard-core doomers tend to miss.

“A dollar may be worth – in buying power – so much today and more or less tomorrow, but a unit of heat is the same in 1900, 1929,1933 or 2000”.

And yet, for the purpose at hand, so what? We call the variation in buying power inflation or deflation, and as long as the variation is not so severe as to convert the dollar into pure noise, we can readily apply a 'deflator'. And for evaluating whether ethanol really produces a return, inflation hardly matters unless it reaches Zimbabwe levels, as many of the key issues seem to play out within a single harvest season.

For example, if a biofuel has a 3:1 EROI then water, land, labor, soil, etc are all assumed to be equivalent ratios in the input.

I can't parse this, can you elaborate just a little? For example, even the Dutch have pretty much stopped making more land, so the notion that anyone with a functioning brain cell would be assuming that there is a 3:1 return of land on land is patently incomprehensible. I suppose they might be assuming 3:1 on something to do with land, but what could that something possibly be?

At some point in the not too distant future, we may run into a shortage of a central good that has no ready substitute. Using net energy analysis, or something similar, will give us a better head start to this event, and more holistic plan alternatives. EROI has many problems. Conventional economics has more.

We'll probably need a whole toolbox, not just a wrench or a voltmeter. However, I'm not fully in sync with the hatred of economics often expressed around here. Like all viewpoints it has intrinsic limits, but at least it examines the world more broadly than through the lens of a single commodity. And even economics can tell us, for example, that if substitutes for oil - a central good for aviation at the moment - become highly problematical, business people will simply need to pick up the phone more often, and physically travel less often. Well, duh.