I'd go for the Cytronex. The first successful application of the Tongxin motor to a mass-produced bike, with no reliability issues noted. Also the best-looking electric bike, and a bike which targets a new segment - fit cyclists who want a bit of help on hills.
In second place would be the new Powabyke, which I don't think should be compared to the Cytronex as they are targeting on different segments and happen to have arrived at the same battery mountin position for different reasons, for bringing decent electric bike quality and style to the mass-market a competitive price.
I'd put the Wisper 905se in at third - only I know it came out last year because John and I bought ours back then! I think it is the best all round hub motor bike on the market at the moment, with Ezee having lost its way a bit.
The Agattu doesn't get into my top three because, although an excellent bike and probably the best all-round crank drive bike, is not that much better than the Gazelle, which beat it to market, and those which have come out since (which AtoB seems to have virtually every edition!). I don't think it would leave a gap in the market the way that the other two might. The Pro-Connect doesn't get in either as I can't work out what it is for!
Special mention for battery breakthrough of the year goes to Li Ping for bringing a new technology to market, providing great support and customer satisfaction.