Ephemera will comfortably synchronize your ebook reader with Instapaper.com via USB. It works with the Amazon Kindle, Sony readers and pretty much any device capable of reading HTML, Mobipocket or EPUB files. By default, Ephemera gets your unread Instapaper news as single articles. Read one, delete it on your reader, and during the next sync it’ll be archived on Instapaper.com.
If you want it to, Ephemera will automatically start up, sync, and then unmount your reader when it detects the USB connection. Configure the app once, and then just have it work for you — by simply connecting your reader!