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, which should cover quite a bit of ground.
It will fetch your news as single articles or in Instapaper’s premade bundles (Mobipocket & EPUB). Personally, I prefer the former. I can read an article, delete it on my reader, and during the next sync it’ll be archived on Instapaper.com.
Being the lazy guy, I’ve also implemented a feature I call “Plug, Sync & Go”: If you want it to, Ephemera will automatically start up, sync, and then unmount your reader when it detects the USB connection. My idea was that you’d configure the app once, and then just have it work — by simply connecting your reader.
Great idea: a Mac app to automatically synchronize Instapaper’s downloads to USB-mounted e-readers. I especially like the synchronization of deleted articles to your Instapaper Archive page.