I use oneNote (Microsoft product). My hubby got me into it and now I'm avid, or is that rabid? Doesn't matter, as It's working for me. I like it for its organization. I can screen shot web pages, or just highlight copy & paste into it.
I have Sections, which has tabs, which has pages its fun!
As you can see, I've got a Tab for my family lines, a Pico Search query info I set up for Crook Co. Or GenWeb (free plug for one of the county sites I write) OK, http://orgenweb.org/ takes you to the state site, (which I maintain) click on counties page to find the individual. I also have a tab for Research Tips. This is where I stuff the cool tips I find on twitter, facebook, just out cruzing the web.
Inside each of these tabs, are multiple pages (like file folders with paper inside) I can keep notes on all kinds of stuff. When you highlight, copy and paste, it automagically puts the url from were you "borrowed" the information.
Now when I put data into MyHeritage Family Tree Builder or Family Tree Maker 16, I have the link where the data comes from, so I can go back to confirm the information. Of course, you have to worry about the data disappearing in the future as people drop paying for their web site, or the data moves to another server and links are not caught up. So this is not perfect, but for now it works.
So, what brought me to this point is from the following link on organizing pictures.
How to add source information to digital pictures. Its worth the read and good for things besides genealogy.
Thanks Beth at genealogydecoded.com its a great idea.