Zotero does let you tag notes.
You can use note tags to differentiate between quotes and your commentary. And you can group tags with saved searches, to separate the notes from the quotes even more.
Zotero automatically names a note by its first line. So, if you put page numbers in the first line, then the notes will be organized terms of them. I don't know if that will work for you, you'd probably just need to give it a try.
One nice thing about Zotero notes is that you can drag them from Zotero and drop them right into OpenOffice.org writer documents (or other text documents, blogs, etc.). In OOo, the note will get the style formatting of the paragraph where it's dropped. So, no more retyping of direct quotes.
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