Earlier this year I explained how to get Instapaper to wirelessly send a weekly collection of articles directly to your Kindle. Of course you can also do this manually by simply downloading the Kindle-friendly file from Instapaper.com and copying it over via USB (or by visiting Instapaper on your Kindle–see Joel’s comment below), but if you’d prefer an automated desktop approach, try these two free Mac and Windows programs.
Ephemera (Mac – 10.6 “Snow Leopard”)
Ephemera is a small program built by German developer Carlo Zottmann. After you set it up, it can automatically launch when you connect your Kindle to your Mac, then download new Instapaper articles and copy them over as individual files to your Kindle.
If you delete the articles from your Kindle and then reconnect to your Mac, Ephemera will make sure they’re marked as archived on your Instapaper account. (Make sure you read this note from the developer to prevent Instapaper from archiving everything after your first Ephemera sync.)
Wordcycler (Windows – XP, Vista and 7)
Wordcycler is Texan developer James Sulak’s answer to Ephemera–he writes that he liked the concept, but needed a Windows-friendly version, so he wrote his own. Like Ephemera, it will automatically copy articles over when you connect your Kindle, and it will keep archived articles in sync as well.
Both programs can send the unread articles over in one big document too, but I’m not sure how or if the archiving functionality works in that case.