blogged earlier about my favorite iPad app, Offline Pages. I've found it to be a lifesaver on long plane rides...provided I take the time to save pages before the cabin door closes.
The more I use Offline Pages though the more I realize it's missing a key feature: highlighting and note-taking. Many of the pages I've saved have interesting excerpts or items I want to blog about or comment on when my connection is restored. There's no way for me to highlight and annotate in the Offline Pages app though and I don't see this functionality in Instapaper either. Given that you're working with an offline version of the page in both of these products I'm thinking it would be fairly easy to add highlighting and note-taking features to both apps.
Offline Pages and Instapaper Pro is $5 but if either one of these implements comments and note-taking I'd be more than happy to pay $5 or even $10 for added convenience.