PDF Viewing

iBooks would seem the most obvious choice.

 

Good reader all day long

 

Good Reader is excellent.

 

iBooks doesn't support scrolling of PDFs, also in landscape mode it just zooms out whole page to fit on screen which is kinda silly.
GoodReader also doesn't support proper PDF scrolling. I don't uderstand how people can call it an excellent reader when it doesn't let you scroll through PDF pages like you do on your computer or on Apple's own internal iOS PDF viewer.
Adobe Reader lets you scroll PDFs, but it also displays same page number popup which cannot be disabled, and a little bit slower than iOS viewer.
There is no perfect PDF reader for iOS.

 

IBooks displays them well. GoodReader has some very nice and robust file organization features, as well as integration with cloud services such as Dropbox and WebDAV. I use it all day long, and keep files synced between my iPad and 3 separate cloud vaults. It's an awesome tool!

 

I use iAnnotate. I think it's an excellent app, but it might be a bit pricey if you don't need a lot of annotation functions.

 

I have had very good luck with PDF Expert.

 

I use that one, too, it's a pretty good app. iAnnotate has a bit more features, but both do the job well.

 

iBooks works killer for me.