Why is there a difference in available energy in saturated vs. unsaturated fatty acids?
The total energy stored in macromolecules is commonly quantified by the amount of $\ce{ATP}$ produced, as $\ce{ATP}$ is used throughout the body to couple reactions and make them thermodynamically favorable. 

First, as the oxidation of a double bond in an fully saturated fatty acid requires a reducing agent, you here produce $\ce{FADH2}$ from $\ce{FAD+}$ which is equivalent to a $\ce{1.5 ATP}$ gain.[1] 

Also, unsaturated fat has double bonds in cis positions that are unfavorable to beta oxidation.[2] An enzyme coupled reaction is needed for the double bond shift. Therefore, an enzyme coupled reaction that requires energy (in the reductant form $\ce{NADPH}$) is needed to make the molecule a trans fat with a shift in bond position in order to continue oxidizing the molecule completely. $\ce{NADPH}$, usually is defined as $\ce{2.5ATP}$ equivalents[1] and this extra energy expenditure in shifting the double bond is why less energy is ultimately produced.  Note, this $\ce{NADPH}$ is only used when unsaturated fats have an even numbered bond position.[2] This happens with polyunsaturated fats when the first bond is shifted. 

For example:

18:2 linoleic acid will yield $1.5 + 1.5 + 2.5 = 5.5$ less $\ce{ATP}$ than 18:0 stearic acid.



References:

[1]: http://www.saylor.org/site/wp-content/uploads/2013/04/BIO101A-6.2.3-CellularRespiration.pdf

[2]: https://en.wikipedia.org/wiki/Beta_oxidation