I've spent quite a bit of time thinking about how I can transition to ebooks for programming reference. I've had a e-paper Kindle for three years and haven't purchased a single physical book since. Typically with technical books I end up writing a lot of comments in the margins, adding page markers with notes on them and highlighting everything.
I tried reading PDFs on a e-paper Kindle and it doesn't work well at all. You can't adjust the font size, page drawing is painfully slow and the device isn't built well for my workflow. Kindles are perfect for relaxation reading, but not that great for much else.
I started looking for an iPad PDF reader and there are no shortage of those. I tried quite a few readers and read about a lot of others.
Adobe Reader (app link)
I used this for about a week. The page flipping speed was ok. It had trouble with large PDFs. Note taking wasn't that great and highlighting wasn't much better. For a free app it will get the job done, but I was looking for something better.
PDF Reader Pro (app link)
This started off as a promising app. Highlighting was ok and it the app was responsive. The problem I had was page turning wasn't that smooth. It had trouble zooming in a page and the interface wasn't that great.
iBooks (app link)
You can read PDFs with this and thats about all. No fancy features here.
Kindle for iPad (app link)
Limited note taking and highlighting. Not that great.
PDF Expert (app link)
This is by far the best PDF reader I have ever used. The interface is really clean and well laid out. It supports book syncing with dropbox so all of your comments and highlights are backed up to the cloud. It also supports syncing with a Webdav Page turning is incredibly fast and supports border tapping and swiping. It will zoom in on a page so you don't see borders and it doesn't clip any of the text. It supports a page grid view so it's easy to find a page if you've lost your place. It supports tabs at the bottom of the app so you can have more than one book open at a time.
I really can't say enough good things about PDF Expert. I was hesitant paying $10 for an iPad app, but it's true that you get what you pay for. Anyone looking for a PDF reader should give this app a try.