One of the wonderful resources shared in Klemmer's HCI course are the articles by Nielsen Norman Group. Specifically, here are three we used to help us evaluate assignments during class. How to Conduct a Heuristic Evaluation discusses how to use a small set of people to examine an interface for usability issues with a list of criteria (heuristics) as an evaluation tool.
10 Usability Heuristics for User Interface Design presents some of the most general principles of interaction design. This list can be a good starting point for what to look for when evaluating an interface.
Severity Ratings for Usability Problems provides a way to prioritize the issues found with an interface.
Next up I'll be using these as guidelines as I search the web to find sites with usability issues.