I don't own one, but I've tried a few, and they're really great basses with top notch quality. I love the ebony fingerboard with the MOP blocks. These basses sound really articulate while still being punchy, and are really versatile. The pickups are humbuckers but look like jazz PU's, and I love how they're voiced. A couple of little complaints from me would probably be the neck-through construction, but that's just me being a bolt-on kinda guy (these things slap like it's nobody's business despite the neck, so no problem there), and the screws on the bridge, which are long, sharp and tend to damage your gig bag if you're not careful. I had a TRB 5PII, and they have the same bridge. It felt about the same as my old TRB as well, which probably means it also has 19mm string spacing.
I think Yamaha basses have always been solid, and I like their newer versions of their models. I especially like the JPII, much more than the JPI, which is already a great bass. I think a lot of people knock on them because the company obviously does more than just instruments; once I showed my old yammie to a friend, who then quipped, 'So did it come with a helmet?'

. No one can deny that a good number of all-time greats played and still play these basses though, and that they are a leading player in the industry because they build basses for every price level that have top-notch build quality and rich sounds. There's ever a cheaper, bolt-on version of the NE2 which is also a great bass. A friend of mine gigs with it almost everyday, and it sounds great.
Lastly, as this is already the longest post EVER, there's a band here in Germany called The Heavytones who play for TV Total, which is pretty much a late night talk show. The bass player (Markus something, I forget, monster player) gets an amazing tone from his NE2, it's not even funny. I couldn't find a better clip, but here it is:
http://de.youtube.com/watch?v=aAolStYSUvM&feature=related
Hope I helped!