I know that many people consider Dragon Quest V or VIII to be the best in the series, and there's no denying that both of those are great games. However, Dragon Quest IX on the DS has to be one of my favourite JRPGs of all time. It's perfectly suited to the console, its design is perfectly suited for the daring narrative perspective that it pulls off (having an entire crew of silent protagonists and putting the focus on the incredibly realized NPC characters), and it's insanely playable and replayable. I love that game so much that in any other year (that didn't have Super Mario Galaxy 2 released in it), it would be my favourite game of the year.
So while some people might be surprised or think that polls of gamers on their favourites in a series will almost always skew towards more modern offerings (and this is true of most media – one only needs to look at IMDB's "best movie of all time" rankings to see this), I think that they absolutely nailed it. Those other games are great, but DQIX is perfect.
You can see the poll (in Japanese, though there's helpful graphics on the side) here.