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The 'grep' command (or others) at the Terminal command line might be useful. However, you'll need to describe exactly what you want to accomplish. "Organize" is far too vague.
 
Have you tried TextWrangler's Multi-File Search? Take a look at the Search and Grep Reference section in TextWrangler Help.
 
Does sound like you need a terminal session, grep and a file redirect oh and possibly find as well. Here's an example of looking in all txt files for the start of a url and putting output into a file

Code:
find -name "*.txt" -print 2>/dev/null | xargs grep "http" > urls.txt

be careful about what you specify in the grep code as you might have to escape out any special characters like ':' or '/'
 
Does Evernote have the ability to organize according to defined parameters?

I am just tryihng to organize my bookmarks by URL. I am trying Text Wrangler now.

Evernote does not.

You'll need to use terminal by piping in the text from the files and use a regular expression to organizing like names.
 
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