I purchased iAnnotate and PDF Expert for iPad. Journal article reading was the reason I purchased an iPad. I wait for the Retina display because I love not having to zoom around the page to read. I lean toward PDF Expert because the interface is more standard, cleaner, and less gimmicky. It's also being continuously developed with frequent updates. Both programs do pretty much all the same functions, and Dropbox (and other cloud services) syncing means you can switch platforms and devices without losing anything. Annotations are written to the file.

(I have no association with either company.)
http://readdle.com/products/pdfexpert_ipad/