Yes, the link should always be captured if it's available. There are no options about that.

I have just run CN 1.5.4 and tried to clip text in Google Chrome (latest version) from cintanotes.com and other sites - the link is captured ok. Please try the following:
1) Try to change the Ctrl+F12 hotkey to some other hotkey, like Win+C
2) Try to clip from some other webpage
3) Try to clip on another PC
And please tell me the results. Thanks!
P.S. I assume that you haven't tried it in Firefox, have you?

Are you sure CintaNotes doesn't already do that?What kind of text copying are you referring to? Clipping via Ctrl+F12 or plain Ctrl+C, Ctrl+V?

Well anyway, thanks for reporting!)

Thanks for the idea!
I agree that the number of options will be growing, so I reckon sooner or later a separate options dialog will have to be introduced.
The approach that you suggest is very innovative, and I see that it will be really great for searching settings.
However, I don't see that it will be helpful enough for browsing different settings. Or do you suggest using tags for this? That would be really cool, but it needs to be really thought out in order to be really convenient. The main problem would be integration of various types of controls. Also unlike regular tags and notes, settings need to be translated. But the idea is awesome, thanks!