IME, it depends a little bit on what the stock brakes are. The pads come with the brakes that come with the bike, so the LBS just assembles what's in the box. I've had very good luck with Shimano Ultegra pads and with Kool-Stop pads. I'd ask your LBS what they recommend for your area.

As for cantis, the ones on my old hybrid were horrible- always rubbing. But the wheels were also pretty terrible- never quite true. So it was a case of the chicken and the egg. The Avid Shorty 6s on my commuter have worked great and rarely go out of alignment, but that bike has better wheels too. It's hard to say what the root cause of the hybrid's brake issues was. I would double-check that your wheels are true and the brakes are set up properly (pads aligned and tight, spring tension, etc.). If that doesn't fix it, maybe it's time for better cantis. I've had good luck with my Avids (though not everyone likes them). The Tektro CR720s get great reviews and are pretty affordable IIRC.