What is the real cost (all costs) in to send a freight craft to ISS? Which launch system is the most cost effective?
The linked question on launch cost per pound is a good starting point. Multiply this with a rocket's maximum payload and you have the true cost of one launch. This is what you'd pay to the launch provider to have your payload launched to LEO. The launch provider uses this to pay for building the rocket, transporting it to the launch site, launch services etc.
Launching to the ISS is more complicated. SpaceX advertises the launch price for a Falcon 9 at $62M. The NASA contract with SpaceX for ISS supply runs was more expensive at ~90M/launch, because NASA wanted extra certification work, and because the launch now includes a Dragon capsule.
For manned Soyuz launches to the ISS, NASA paid \$70 million per seat in 2013. This seems to include a certain amount of price gouging and/or subsidies, because you can buy a generic Soyuz launch for in the region of $60M.
Launch costs have always been difficult to calculate. SpaceX publishing them on their website has made it a bit easier, but I don't see Roscosmos putting the sticker price for a Soyuz on their site quite yet.