Port Royale 3 - pretty darn awesome. It is kind of like Pirates! meets Tropico, which is not a bad thing, the city management is not as complex as Tropico, but there is enough evolution that it doesn't seem boring and not overwhelming either. The graphics are very nice and smooth and music is nice chill out type. Hopefully they pick this one up for a flash deal but if they don't I think it is worth the existing discount price.
The core of these pirates games is kind of buy cheap, sell high, but it is pretty fun and addictive way to kill time.