For references on web pages you can use the bookmarklet I have called W?. However that only works on web pages, not in PDF files.
Qiqqa is a good program to work with references in PDF files directly, but you have to handle them one-by-one. Here is how to do it:
- Install Qiqqa (requires Windows, unfortunately).
- Add your PDF file to Qiqqa (the Local Guest Library works fine for this).
- Open the PDF in Qiqqa.
- Click on Metadata (in the column to the right of the PDF in the current layout).
- Then click on Sniffer.
- In Sniffer you can just select some text an Qiqqa will use that to look it up in Google Scholar or PubMed (you can choose).
For more about importing references from a PDF files to Zotero see the discussion Zotero Forums – Importing the references from a PDF files.