-- N800 has 800x480 screen, N560 has 640x480 screen; more resolution is always nice
-- N800 is somewhat larger
-- Speaking of keyboard, with no external keyboard the N800 has an apparently quite usable "thumb keyboard" touchscreen mode. The N560 figures you'll be using a stylus.
-- N560 has a built-in GPS receiver! N800 could pair with a BT GPS receiver -- I have a GPSlim 236, which people report the N800 works with -- but more importantly, there's already a handful of high-quality, commercial mapping/navigation programs for PocketPCs. I use Mapopolis, whereas TomTom is probably the most popular. Nokia just announced some mapping software, but only for Europe... and I'm in the U.S.
-- Both seem to be OK at reading PDF files and running a remote desktop client if need be.
-- N560 has Pocket Excel/Word... N800 has... ???
-- N560 has IrDA, N800 doesn't. I've used IrDA in the past to print photos from my phone -- nice little feature, and printers with IrDA still seem a little more common than those with Bluetooth or WiFi.