The way it is being done is quite simple, but it involves a group of people or someone with a lot of alts. They camp systems where they can predict the way you are going to travel say between Amarr and Jita; this is the key. The easiest way to explain this is to make a simple diagram.
The scanner scans and identifies the person to be ganked (on gate A) while they are aligning to the next gate (Gate:B). He then communicates the target to the gank team sitting in the next system. The team will wait for you to jump threw gate B, and they will jump you while you are aligning to the next gate (Gate C).
The ganker will probably be in a battleship fitted with as many sensor boosters and amplifiers as he can fit for a wicked fast targeting. They will also have a warp scram, and this will serve as a dual purpose. First, it will stop you from warping away (assuming u don't have warp stabs). Secondly, it will stop you in space, and make it even easier to hit you. The team also have someone to haul away the loot. I guess in theory there could be someone to remote sensor boost, but i'm pretty sure they would be concorded as-well.
How to protect yourself?
Fit your ships - if your going to be hauling expensive things, then drop the cargo expanders. Go for the agility mods (inertia stabilizers) and warp stabs. Fit a high buffer tank so you do not killed in the first strike.
Dock and unload - If you get scanned, warp to a station and dock. If you don't care about losing a indy then unload your cargo quickly and see if they still try and attack you on the other side of the gate. Remember the scanner already called you out as a high value target; and they might have been sitting at the gate for a few hours looking for a kill. WARNING: There is a small chance you might poded; warp away quickly - don't loose your implants.
Freighters - God awful idea for small items, but it takes a lot to gank it. I would say that if your hauling under 5-6b in one go ahead and autopilot and go watch tv. People hauling 20b+ need to remember that a single ship could probably keep you from aligning somewhere. This means his buddies have all the time in the world to organize a effective gank.
Courier Contracts - 1-2 mil reward for someone else to haul your stuff? Yes, please. The reward size really depends on what your hauling and where to. If it requires someone to take a freighter into low sec, then your contract might not get filled for a 1-2 mil reward. Be sure to place a high collateral as well. I generally do sell order price + 50%, but everyone has their own little method.
Orca - You can not scan anything in corp hanger bay. AFK away?
Cloaky Hauler - If you are hauling small amounts, then you can't go wrong with a cloaky hauler. Properly fit, it should be entering warp right when your gate cloak drops from you trying to enter warp.
Auto Target Back - A lot of null sec players will have this turned off, but it makes it pretty easy to know if you have been scanned. Just be sure to turn it back off when you get back to null.
Passive Scanners - Just because you haven't been targeted doesn't mean you haven't been scanned. Try and watch for the scan animation.