The "classic" popular size is the Leaderboard 728x90, which currently has some of the highest Engagement numbers on the Cubics network. 728 basically takes the full width of the canvas page and provides for good visibility. Based on the layout of your app you may prefer something on the side. The 120x600 (Skyscraper) is a thin vertical bar that goes well on the right-hand side of the canvas.
The 300x250 and the 468x60 can also be useful, but they really need to be worked into the layout on a MySpace canvas or they're just hiding.
Running an A/B test is the best way to get meaningful results. Brands definitely prefer the 728x90. But start with one of these two ad sizes (728 or 120) and go from there, the best way to know is to test regularly.