If the documents are tagged properly, the copy/paste would work. Sounds like some of them aren't.
There is no solution using the free Reader software but you may want to try a PDF to Word converter such as http://www.pdftoword.com/
(I don't use or endorse that particular converter. Just found it doing a search and used it as an example)
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Well, this may be a bit late given that I am replying more than 4 years after the question was asked... but I think I have found an answer.
My document has line numbering for aligned along the left margin for every single stupid line in this document. So after some trial and error, I used the crop tool found under Tools/Advanced Editing, and simply cropped the page so the line numbers were not included. From there, I simply copy/pasted the text I wanted into a new word document.
While I imagine this is not helpful to the original poster - unless he/she is VERY patient - I hope this answer will be helpful for future users who may encounter this issue. And while I'm at it... HELLLOOO FUTURE USERS!!! Send me a note if/when you read this and tell me what the future looks like! Are we all driving flying cars now?
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The unfortunate part of this advice is that it won't work for Adobe Reader. Cropping is a function of Adobe Acrobat.
And, hello from the not-very-distant future.