Ochanomizu is the place to go in Tokyo if you're into music. It's not as fashionable as the bleeding edge of punk and goth that hangs around in Harajuku, but it's where all the college kids who need a guitar go.
Get off at the station and wander a bit. Right there in Ochanomizu are two great things: CD stores and guitar stores. There are five different branches of Disk Union here around the west exit of the station. Each of the five stores houses a different genre. For example, make sure you're going to the jazz/classical branch, not the five-stories-of-metal branch if that's not what you're into. There are also a lot of used CD stores in the area.
Best of all are all the guitar shops. This is where you go in Tokyo if you're a broke ass student and need a guitar. Seriously, you can hardly take a step before you're running into another guitar store. New, used, stores that have a range of companies, stores that have just one brand. It's a little trickier finding a place that sells a good range of guitar cases, but there is one shop that I know of, hidden up on the fourth floor of a building on top of (yet another) guitar store. I purchased a quality soft bass gig bag and, for use on the plane home, a great hard case for around Y3000. Even in Tokyo deals can be found.
Plus, who can resist the name. Ochanomizu = tea water