Diigo is a bookmarking tool that works great on the iPad. Diigo Homepage

Once you have created an account, you can then access pages that you have bookmarked on any computer from any other computer. You can tag each of your bookmarks with relevant terms, ensuring that you can easily find information you are looking for.

Educators can get special accounts that allow them to link to their student accounts:
Diigo for Educators

Diigo has a bookmarklet that can be installed into Mobile Safari on the iPad which allows you to highlight and save pages you have seen on the iPad. This prevents you from having to e-mail links to yourself to read later, etc.
How to Install the Bookmarklet (go to link on iPad to install).