I find GoodReader to be very versatile and easy to use. I have seen some recent reviews praising PDF Expert, but I am not sure its features are good enough value for the price. When I first got my iPad I also got the iAnnotate PDF app, which is also very good. I still use it for some items.
In brief, there are a lot of good PDF apps available. It helps to seriously consider what your needs are before deciding on a purchase.