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I am trying to organize a bunch of my text docs from over the years that have hundreds if not thousands of urls, bookmarks, and the random note. It's been mostly a headache trying to go through all of it through TextEdit, Microsoft Word and TextWrangler.

Is there an app or a way to better use these apps make this easier by organizing lines of text into groups with certain parameters (ie: find all links with the url 'macrumors.com')?

Have you tried Evernote? Since it seems like you're trying to maintain a lot of notes, it is a good app for that. You can also run it on multiple platforms.
 
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