What's the typical cost (and its breakdown) for a long-haul commercial flight?
Fuel

The fuel consumption of the A380 is about 11 metric tonnes per hour. With a fuel price of \$1000 per metric tonne, this results in \$11000 per flight hour. 

Amortization

An A380 will cost about \$350M. The aircraft will be used for about 25 to 30 years, but let's assume the amortization period is about 20 years with a residual value of \$50M. With an interest rate of 5%, you would pay about \$24M per year. 

That is about \$2740 per hour, or \$0.76 per second, flying or not. 
Assuming a usage of  60%, taking into account turn around times at the gate and maintenance downtime,  it boils down to \$3915 per flight hour. 

Crew

Captain costs \$160K per year, the F/O \$90000. Let's assume they fly about 60 hours per month, the combined flight deck crew cost is about \$350 per flight hour for the base salary. Another \$80 needs to be added for allowances bringing the total to \$430 per flight hour. 

Cabin crew rate would be around $40 per hour, so for 20 crew the cost will be \$800 per flight hour.  

Also allowances for overnight stays and hotel costs need to be taken into account

Airport charges

These vary extremely between airports. You can basically break the costs down into costs related to the aircraft, the passengers and various taxes by the government. 

Aircraft cost usually are related to the Maximum Take-off Mass (MTOM) of the aircraft and the noise category. A Boeing 747-400, while less heavy than an A380, will in some cases be more expensive due to the higher noise level. Many airports differentiate between peak and off-peak hour landings. 

I can't find accurate data for the A380 but an old table that I have for the Boeing 747-400 suggest that total the cost vary between about \$6000 to \$25000. 

Overflight charges

Fees are levied by countries whose territory is flown over, mainly to cover ATC cost. The cost is typically based on the distance flown and the MTOW. For a 747-400ER over Europe, the fee is on average 145EUR per 100km. Assuming an average speed of about 900km/h, the hourly cost is about 1300EUR/h. These costs are lower over the high seas and over the US. 

Rough total

Based on the above, the total will be between \$22,000 and \$41,000 per hour.