The basic principle is that your advisor has control over
everything, and you have control over
nothing. Need an important collaboration for your next paper? That won't happen without your advisor's support. The same goes for access to specialized equipment or supplies (the budget can become very tight when your PI doesn't like you). At most schools, your PI also controls your funding; you can expect to TA more often if s/he doesn't like you.
Your PI knows the weaknesses in your research and knowledge better than anyone, and can use this to your disadvantage. I've witnessed faculty who aggressively attack their own students during examinations (a truly disastrous scenario). More often, advisors will simply fail to defend their poor students from unfair attacks by other faculty. Departmental lectures, defenses, oral exams, etc. are remarkably subjective affairs, and one bad comment can snowball into an event that will add years to your time in grad school.
Another very common tactic is for the PI to hand out the best research projects to favored students. There's nothing so demoralizing as watching a first-year grad student get an publication in Science or Nature (by being assigned to an already successful project), when you've worked for years on failing experiments. I've seen this happen too many times to count.
Like I said, there's no way to list all of the different ways that your PI can make your life painful. It's just an extremely unbalanced, unregulated power relationship, and with any creativity at all, an advisor can use that power to destroy you.