@Thomas,
I agree... frequently I will read something in the paper paper, look for it online for some reason (grabbing a quote, usually), and then when looking for it on the NYT website find other stuff that I hadn't seen in the paper paper (even though it was there, I just missed it -- though there is online-only content too).
The converse happens too though, like when I'm away from home and read the NYT online and then come home and catch up with the paper paper. I like having access to both. (Thanks, mom, for your annual Christmas present. Much appreciated.) Basically, I find the online version much easier for
researching something specific that I want to learn more about, while I find the paper version is easier for general-interest browsing, coming across things that I wouldn't expect to be interested in but nonetheless enjoy reading.