I am taking up Zotero and so will gather the tips I come across here.
Zotero can allow you to archive great NY Times articles for use and reference later. NYT generally offers a permalink for articles. If you want the whole article in Zotero, not just the permalink and not just the first page (since NYT articles are broken up that way), one Zotero forum post suggested you find the “print” option in the article and then take that page into Zotero since it won’t be broken up. If you do bring in the whole article as a page “snapshot,” you will be able to annotate (’nuff said).
Don’t forget to tag it a few times when you first bring it in; when are you really going to go back and re-tag? Now or never.