1. For those books that support the HTML view, I've read them in the browser from the Safari Library web site. These have been excellent, including diagrams and code snippets. One or two books have had slight formatting problems (a line of example code not wrapping).
2. For books that don't support the HTML view, or books that I've downloaded as PDFs (part of the my subscription is a certain number of "download tokens" that can be redeemed to download chapters or whole books), I've read then in GoodReader. This has worked out fine.
3. Finally, they offer some books for download in EPub format. I've tried those in iBooks, and they've been good. I've also used the free program Calibre to convert some of the PDFs I downloaded to EPub and they have worked fine.
I am quite pleased with the combination of O'Reilly Safari Library and my iPad.
Oh, they've also announced that this summer there will be a Safari Library iPad application. That should be interesting.