When I'm germinating, I like to take my seeds and put them inside a matchbox, put a like-sized emery board inside the box, and shake it for about a minute. This scuffs the outer coating of the shells, and is rumored to make water absorption a little bit easier.

I don't like germinating in water, simply because I am sometimes gone all day at work, and I don't like leaving the roots exposed to water (and no oxygen) for long periods of time. If you're going to use this method, just make sure you're using distilled water in the cup.

I always use the paper towel method, and sow directly into soil as soon as the taproots emerge. I don't like waiting until they're 1/4-1/2" long, or whatever...it's just too risky to disturb the roots when they're that young & that sensitive. I generally have a 90-100% germination rate, by the way.