How do I choose a lab to rotate in? Normally, graduate students at my university go through three rotations. I've done two and will need to choose a permanent advisor after this next one. So choosing a rotation is similar to choosing an advisor, yet the philosophy can be slightly different.

1) Funding: Does the PI have funding for at least one year? Having that planning time to find other sources of funding without having to TA is indispensable.

2) Choosing a permanent advisor: The purpose of a rotation is to find an advisor and lab I am comfortable working with, as this will lead to a happier and more productive few years of my life.

3) New skills: Doing rotations in multiple labs will give me perspective. I should be learning different skills from each rotation.

4) Research interests: I should find a lab with research interests that align to mine. I don't want to be stuck working in a field I don't enjoy for the next X years.

5) Prestige: An advisor with strong industry connections can leverage those connections to help me break into industry or finding funding for my startup. A recommendation from a professor famous in your field can be my ticket to a tenure-track position. 

How should I reconcile these different points? I'm a bioinformatics grad, if that makes a difference.
I would focus on choosing an advisor and a project as your priorities. These will be the two most important decisions you make as a graduate student. The project you pick will be your preoccupation for the next five or so years, and your advisor will be one of the most important figures in your career. New skills and funding are secondary to these, and the issue of prestige almost shouldn't enter into your decision at all.

In particular, I would actually argue that it's not just choosing an advisor; it's choosing an advisor and a group. You will almost certainly be spending more time with your fellow group members than with your advisor. Therefore, you need to make sure that you can get along with both your advisor as well as your future colleagues. A miserable working environment is not worth the trouble, if another viable option is available. 

Also, make sure that the project you want to work on interests you; it'll drive you to accomplish more, and you'll be better motivated to make it your own (which is what you need to do to succeed as a graduate student).