Are fossil fuels really formed from fossils? Hydrocarbons have been found in great abundance elsewhere in the solar system where there is unlikely to be evidence for life past or present.  No fossils involved.

Petroleum and natural gas wells that have gone dry 50 years ago, are found replenishing a fraction of their output.  No fossils involved.

Vast biomass of micro-organisms and extremophiles beneath earth surface estimated to be several times the size of the surface biomass found deriving their chemical energy for life from methane and oxygen pulled from sulfates and ferrous oxides.  The source of methane way too deep to come from fossils.  No fossils involved.

These recent findings and other evidence were foretold by the late scientist and researcher from Cornell, Thomas Gold, who authored "The Deep Hot Biosphere, The Myth of Fossil Fuels".

After seeing evidence of extremeophiles in relative abundance in even the deepest of mines, Gold ties the sub-surface biosphere to the "Deep Earth Gas theory" to show a more plausible primordial explanation of hydrocarbon fuel formation than the generally accepted "fossil" theory.

He posits that 
"Hydrocarbons are not biology reworked by geology (as the traditional view would hold), but rather hydrocarbons are geology reworked by biology."  In other words, as in Saturn’s moon Titan and other hydrocarbon rich areas of the solar system, the source of hydrocarbons is primordial; but as they upwell into earth’s outer crust microbial life uses it as energy source.

While the details of the Deep Earth Gas Theory are beyond scope of elaboration in this question area, the main points which Dr. Gold supports, and provides evidence for are: 


Hydrocarbons are primordial. IOW, hydrocarbons like elsewhere in the solar systems are here since the planet's birth.
The earth was subjected to only a partial melt.
Hydrocarbons are stable to great depth.  High pressure greatly stabilizes hydrocarbons against thermal dissociation.
Rock at depth contains pores.
Primordial hydrocarbons are still upwelling from the deep earth.


some sub-points worthy of mention:

It more adequately explains why Helium is only present in the earth at any mine-able quantity in natural gas.   There are no pure Helium wells.  Why the strong association of hydrocarbons with Helium, an inert gas that can have no chemical interactions with fossil organic materials or with hydrocarbons?  This is known to geologists as the "Petroleum Paradox" and cannot be explained at all by a sedimentary origin of hydrocarbons.

The presently accepted theory of fossil fuels is that the hydrocarbons formed from the decayed remains of ancient organic matter (fossils) that somehow sank down into the deep earth and got trapped in sedimentary rock formations where increased pressures assisted in converting the organic material over time to hydrocarbons.

Well, hydrocarbons are found in depths where no surface life remains could have possibly geologically submerged to.  The physics of how the ancient organic materials or the resulting hydrocarbons sank deep into the earth have yet to be explained.  Also, hydrocarbons have been found in igneous rock formations, which the accepted surface to sediment theory cannot explain.

Can we still say that fossil fuels are really from fossils?
Let's look at this. A very large number of points for one question.

First, the solar system. We do not see any hydrocarbons in the inner solar system (Mercury to Mars). This is because in this region of the solar system, dissociation by solar UV rapidly destroys primordial hydrocarbons.  This effect is much weaker further out.

Oil well 'replenishment' will happen to some degree over several decades, just from internal migration of oil. Typically only a certain percentage of oil in place is recovered, with the rest left in isolated pockets by the water flood. Give it a few decades and these oil pockets will tend to remigrate and link up, giving the appearance of replenishment.

I'm not sure what you comment of The source of methane way too deep to come from fossils. No fossils involved.. That's an unreferenced assertion.

Helium is present in Natural Gas as a result of accumulation of alpha-decay particles from radioactive isotopes; we can see this from the massive enrichment of Helium-4 over Helium-3. It's not a paradox; geological structures that can trap methane will also trap helium.

The current theory behind petroleum geology is that source rocks with a high organic content (often containing biological hydrocarbons from algae and leaf waxes) are buried in sedimentary basins; at temperatures around 100-150 degrees C this kerogen breaks down to form crude oils (this is verified in the lab). Oil then migrates out of this source rock; if it encounters a trapping geological structure, which need not be sedimentary, then it accumulates as an oil deposit. Gas is similar, with a wider range of source rocks.

The physics of how this happens are well known and established.

I would also note that we don't see hydrocarbons coming out of mantle-derived volcanoes such as at Hawaii. This is a major problem for any theory of primordial hydrocarbons.

Additional Points

First, it would be nice if you provided references rather than a link to a book to buy. 


If hydrocarbons were primordial, then we would expect to find them mostly in areas where the mantle or mantle taps reach the surface - mid ocean ridges, and ocean island volcanoes. We don't. The major oil fields are located in continental extensional basin settings. 
There is plenty of evidence for mantle outgassing - including all volatile species such as hydrocarbons - in the first few hundred million years. Furthermore, on geological timescales the mantle is still undergoing vigorous convection and can be considered liquid.
Is irrelevant.
This is simply wrong, if referring to pores that can offer any support against pressure. The crust becomes ductile at about 10-15km, and the mantle at 60+km, meaning that conventional porosity cannot exist. 
See (1). For the Earth, outgassing was essentially completed billions of years ago, as we can see from isotopic evidence (and I suspect that the moon-forming impact didn't help).