I don't do this much, but I can tell you how I would do it; given the apps I currently have on my iPad.
I would use a combination of Safari, Evernote, the
Evernote bookmarklet, and Skitch.
When I need a bit of something from a webpage, or even the entire page I'd use the bookmarklet to send it to Evernote. This can take some time with an entire page, but it is fairly fast if you only send text.
When I need to make a comment or highlight something on a page I'd zoom/position the view and then take a screen shot; then switch to Skitch. I can then markup the screenshot, add some explanatory text, and send it to Evernote.
If I've got a good internet connection I can also switch to Evernote itself and add additional comments (audio, text, pictures).
Once all three apps have been launched you can use the four finger swipe mentioned by zphone to quickly switch between them.
It would not surprise me to find that there are other app that would to as good or better a job. For that matter I keep talking myself in/out of Circus Ponies Notebook; though the primary appeal here is that I already have and love this app on my iMac. So shop around. You'll probably find multiple solutions.