I don't remember if any one ever found an app that would directly annotate a power point.
However there are several ways to convert a power point to a PDF, and there are loads of choices when it comes to annotating PDF files.
I believe iAnnotate is among the most popular for the college going crowd. I like PDF Express, but it's more general in nature. Not particuallyr optimized for note taking.
For converting power points.
If you already have Pages, it can import a power point and export as PDF.
PDF Converter is also a decent choice, and can convert directly from a file on DropBox.