And here are some more sources:
The granddaddy of them all, that has all the gnarly scientific details and formulas that the nukemapper site uses is
The Effects of Nuclear Weapons, 640 pages...
Some other ones are:
The Effects of Nuclear War, which was used by GDW when drafting
Howling Wilderness
The Medical Implications of Nuclear War, another brick at 638 pages...
Survival of the Relocated Population of the US After a Nuclear Attack
an answer to your specific question, Raellus:
Minimizing Damage to Refineries from Nuclear Attack
The Effects of a Nuclear Attack on Rail Activity Centers
And how to plan a nuclear war (!!!):
The US Nuclear War Plan: A Time for Change, which goes into details about things like the "hardness" of various targets and what it means to say "Well, X Target got nuked".
and (this is a repost from the original site, which gave me a security error), Stuart Slade's
Nuclear Warfare 101
and
The US Army's
FM 101-31-1, Nuclear Weapons Employment Doctrine and Procedures, which gets into the nitty-gritties of how to determine which weapon to use to achieve the objective.
Longer term I've been toying with the idea of a piece on the nuclear phase of the war... but the above documents combine to equal some seriously depressing reading.