I'd agree with this.

My choice is transit.yahoo.co.jp There's no English version, though.
You can adjust results based on how fast/slow you can negotiate any tranfers, plus the results provide handy links which easily let you identify later trains for the given station.

For me, Hyperdia's only advantage is that it lets you screen out bullet trains that JR Pass is not valid on. So I only use Hyperdia if I'm using JR Pass, which is rare.
But for non-Japanese readers, I would think Google map + Hyperdia is good.

Anyways, sorry this is getting off-topic...