Electrical – quickly charge supercapacitors with a power adapter

Humourous, but once you look a little bit below the surface, the absurdity of the idea is hard to ignore.

(1) is possible, but USB ports to my knowledge are current-limited, so no permanent damage should occur.

(2) is the most likely scenario, for a different reason than you describe. The 5V coming out of the USB port is well below the 12-18VDC that a typical laptop wall-wart provides to the computer. The negatives are most likely already common (connected together) inside the unit. Many laptops require communication with the power supply before power is allowed to flow as well (locking out knock-offs and other, incompatible equipment).

(3) could only be possible if the laptop was intended to take +5V input, and if the USB port could source whatever current the laptop wanted. Even if these two things were made 'possible' by the electronics gods, the major issue still remains. Energy transfer is lossy. Any benefit gained from power coming in is more than negated by the energy wasted getting it there. Not to mention, the energy that arrives at the inlet would have to be converted / transferred before going back to the batteries / USB ports, wasting more energy.

An efficient way to charge high capacitance capacitors with a small current is to use an inductor. i.e., you see the technique all the time in voltage converters. i.e., charge an inductor field by placing a voltage across it, thus building up the current in the inductor. Then, place the inductor in series with the capacitor that you want to charge. I.e., high speed switching. The inductance in the inductor will limit the current, while the energy stored in the inductor field will cause the voltage of the inductor to change to meet the voltage in the capacitor that you want to charge. i.e., at the point where you stop charging the inductor, and place it in series with the capacitor, the inductor becomes a current source. You probably remember hearing in your first AC electronics course that capacitors resist a change in voltage, and inductors resist a change in current. These characteristics make them a perfect combination for solving your problem...