it all depends on what sound you're shooting for. some guys I know really like the EMG sound, but it's not my personal thing even though I really tried to like them.
in establishing which pickups I would use as my standard install I tried all of the major suppliers and also a whole lot of the boutiques. I found that I preferred the Nordstrand sound - and nearly 100% of my clients agree. for a Nordy P/J set you would need to decide if you wanted a single coil for the J pickup or whether you wanted a split-coil. the split coil will be hum cancelling, even when run solo
more info can be found here: http://www.nordstrandpickups.com/bass-pickups/traditional/traditional.html
in the end it comes down to what your ear prefers. I'd recommend heading out to Guitar Center and playing a few basses with EMG's and see if you like the sound.
all the best,