App for offline bookmark reading on iPad
I really like Instapaper. Not only does it allow storage and hierarchical organization of seemingly unlimited bookmarks/pages, it has a nice, big cache and reading offline works like a charm.

It will save articles that are broken into multiple pages automatically which I particularly like.

It also sports an iBooks-like UI which allows typographic control, strips ads and fluff out, and helps with the reading experience. Frankly, I prefer reading in Instapaper than on the original site.

Lastly, it keeps track of where you left off in multiple articles if you don't finish one and move to another.