I have heard multiple different pros/cons of all the methods.
I have only successfully germinated once, working on my 2nd now.
I did it successfully my first time with Paper Tower
Pros and Cons:
Soaking in water - Pros: easy to watch progression, pop in soil when they sink to bottom. Little risk to seed integrity as far as the Taproot goes. Cons: Theoretical high potential for drowning the seed, you do not want to keep it in the water for 24 hours+ (supposedely)
Paper towel - Pros: Easy to do, soak towels and keep them soaked in a plastic bag, little risk as far as overwater goes. Cons: Potential to damage taproot when doing the transplant/taproot can grow into paper towel
Germinate is soil/Rooter/seed starter - I am told this is the best method, with the only downside is that you can't directly see the progression, and you have to do the 'tride and true' method of waiting for the seed to pop.
As I said, I have only done the paper towel method, but these are the notes I have taken from the other methods. Perhaps other members can provide more insight!