We've got a pretty small desk ourselves, and have recently downsized our home office setup to a laptop from a previous large desktop tower (MacBook Pro review coming soon!). We've found that using a USB dock/hub really helps keep our desk clutter-free; we're fond of our BlueLounge SpaceStation, though we wished it could somehow eliminate the power input and mini Display Port cables too. Another organizing accessory we'd love for our desk is one of these Belkin Grommet USB hubs. Anything that reduces cable clutter is a big plus when organize a compact home office.
Consider using corner or wall space if your desk is facing against a wall; you can find cheap corner shelves at KMart or Target (or online, like we did), and IKEA has an assortment of affordable shelving that could sit above your setup.
A small footprint light that happens to operate off USB power like the Conof USB Lamp might work well at optimizing space, offering light and also a place to recharge your peripherals. And if you have a secondary monitor like we do, consider wall mounting it (we need to do this ourselves this weekend).
If you're in the market for a printer, purchase one that can be used wirelessly or via network, and position it underneath your desk or in another room. position your cables and power strip underneath the desk, like shown here or here.