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1. Expendable Supplies
2. Environmental damage during Extraction, transportation and refining
3. Environmental problems during usage

1. Expendable Supplies
Peak Oil - Oil depletion and future energy scarcity -
Fossil fuels take millions of years to make. We are using up the fuels that were made more than 300 million years ago before the time of the dinosaurs. Once they are gone they are gone. World oil production peaked according to many estimates. This does not mean that the world is running out of oil: it means that we are running out of the cheap pumpable oil that has fueled the economic development of the 20th Century. See: Peak Oil.

Ground water contamination during the gas drilling technique known as hydraulic fracturing, or "Hydro-Fracking."

Mountain top removal / valley fill coal mining (MTR) has been called strip mining on steroids.
In addition to deforestation the process creates a dangerous coal slurry impoundments, often built in the headwaters of a watershed. The slurry is a witch's brew of water used to wash the coal for market, carcinogenic chemicals used in the washing process and coal fines (small particles) laden with all the compounds found in coal, including toxic heavy metals such as arsenic and mercury.
The health problems caused by exposure to these chemicals and heavy metals include elevated rates of mortality, lung cancer, and chronic heart, lung and kidney disease, organ failure and learning disabilities.

EPA is communicating comprehensive guidance to its regional offices with permitting responsibility that apply to pollution from surface coal mining operations in streams and wetlands. The guidance details EPA's responsibilities and how the agency uses its Clean Water Act (CWA) authorities to ensure that future mining will not cause significant environmental, water quality and human health impacts.
See: EPA Issues Comprehensive Guidance to Protect Appalachian Communities From Harmful Environmental Impacts of Mountaintop Mining. 4/1/2010
YouTube - Mountaintop Removal Coal Mining in West Virginia
Mountain Justice - What is Mountain Top Removal Mining?
Our hunger for fossil fuels is affecting the oceans

Coal problems:
As of 2008 69% of U.S. residential energy use was from electricity and 48% of electricity was generated from coal. 37% of all U.S. CO₂ emissions were from coal.
When coal is burned, carbon dioxide, sulfur dioxide, nitrogen oxides, and mercury compounds are released.
Acid Rain:
Sulfur dioxide (SO2) and nitrogen oxides (NOx) are the primary causes of acid rain. In the US, About 2/3 of all SO2 and 1/4 of all NOx comes from electric power generation that relies on burning fossil fuels like coal.

Acid rain causes acidification of lakes and streams and contributes to damage of trees at high elevations (for example, red spruce trees above 2,000 feet) and many sensitive forest soils. In addition, acid rain accelerates the decay of building materials and paints, including irreplaceable buildings, statues, and sculptures that are part of our nation's cultural heritage.

Nuclear problems:
In addition to waste disposal and accidents like three mile island, some of the older plants which use river and bay water for cooling are killing fish. In 2010 several were being required to add cooling towers which cost around $1 Billion.

The nations oldest nuclear power plant, Oyster Creek in the Forked River section of Lacey Tonwship NJ, built in the '60s, has been ordered by the state EPA to install cooling towers instead of relying on water from the Barnegat Bay which kills billions of shrimp and tens of thousands of fish, crabs and clams each year.

New York Denies Indian Point [nuclear plant built in the '70s] a Water Permit because of fish kill and water contamination.

Links:
KXL Pipeline
Air Today, Yesterday, and Tomorrow from Vision Air Consulting.
The Energy Story - Chapter 8: Fossil Fuels - Coal, Oil and Natural Gas