From a purely mechanical point of view...
1. Monk. They have tons of abilities, but none of them really help you until you get some levels under your belt. You're extremely mobile, yes, but your damage output isn't all that good and you're unarmored--not a good place to be in melee. Things get interesting once you hit fifth level or so, but the early levels are a challenge. A monk with the right skills (Climb, Perception, Stealth) can be an awesome scout if you're not terribly concerned about their ability to find and disarm traps. Evasion and improved evasion helps meliorate this somewhat, and multi-classing into rogue can be an attractive option for a monk.
2. Bard. The bard does several things, but none of them particularly well except for having scads of social skills. In an urban setting or intrigue-based campaign, a bard can be awesome, but in most campaigns, they vacillate between being subobtimal dabblers and just sheer dead weight. You have to really twink out a bard to have them be more than a supporting character in anything but social situations. I actually have a bard in my current campaign, and he's really surprised me by being as useful to the group as he is. I think the player understood the challenges of being a bard and made some good choices to beef up his performance.
3. Ninja. I don't mind the concept of a ninja class. I don't like the ninja presented in Ultimate Combat because it's basically better at being a rogue
that a rogue is. They get tons of cool ninja abilities like a ki pool, light steps, no trace... and they can select any rogue talent. The only thing that a rogue gets that a ninja doesn't is trapfinding--in every other way, the ninja is clearly superior.
The following are the worst from a roleplaying point of view. In all fairness, I don't think that the classes themselves are designed poorly or have any mechanical or narrative flaws--they just seem to attract the goobers for some reason.
1. Bard/paladin/sorcerer, or any other Charisma-based class with an emphasis on social skills. This isn't a phenomenon unique to the Pathfinder RPG, but there are people that want to play characters with strong Charisma scores and social skills as a means of forcing the party into doing what they want. From the bard that insists that she is the party leader "because I have the highest Charisma" to the sorcerer that casts charm person on anyone that disagrees with them... It's an odd paradox that people with no social skills try to gravitate toward social roles. Maybe I don't understand it, or maybe I understand it too well, I'm not sure which.
2. Magus. I think that the magus class is reasonably designed and interesting. It's a bit annoying, however, because there are a lot of people that want to play magi because they think that a magus can fight as well as a fighter and cast as well as a wizard. They get disappointed when the GM holds them to the class' limitations. The first game I saw with a magus, the player thought that the magus' spell combat class feature gave him an extra action every round--he kept trying to "cast, then move, then attack," despite the clearly-worded "full-round action" thing in the spell combat class feature. The last session I played with a magus, the player kept trying to talk the GM into letting their magus character cast spells without provoking attacks of opportunity, because otherwise, "the class is useless." He got a bit frustrated with the GM when the GM explained how casting defensively and concentration checks work and referred him to the Pathfinder RPG core rulebook about it.