Hi mate, yes I've been many times now and heading back in 3 weeks time. The first time I went I had a lonely planet Japan guide, and a lonely planet Tokyo guide (and a lonley planet tokyo pocket city guide). all of them had their uses on that first trip. I also have the lonely planet phrase book which is ok too. but after studying japanese now for a few years at sydney uni I haven't used it in a long time. there is another awesome book which I'm trying to track down which is an english book of the rail system maps. this doesn't sound that exciting but there are dozens of rail companies in japan and even in tokyo there is probably half a dozen and lots of different lines, and then the subway too... english rail map is a must, but whilst the JR one is easy to get some others are not always available.
if you are going for the first time, and don't speak much japanese i would take:
lonely planet tokyo
and if you are going outside of tokyo take lonely planet japan too
and a phrase book of some kind.