Going with a notebook doesn't mean you have to use the built in screen, keyboard, and trackpad. For about 5 years, I used only notebooks attached to desktop monitors, keyboards and mice. The convenient thing for me at the time was that one portable machine was my main system both in the office and at my home office.

Though if you have no intention of ever using the system as a portable, you can look into desktops that use mobile parts. You would get the same power efficiency benefits, without the extra monitor, battery and other components going unused. The Mac Mini for example uses 0.24W while off and plugged in, 1.45W while in sleep mode, and 9.14W while fully booted and idle. At absolute maximum, the system will use 85W. With the age of your current system, a modern Mini is likely to also bring more CPU and GPU performance. An alternative small form factor system is the Dell Inspiron Zino. Just be careful there, as some of the lower end configurations use AMD chips similar to the Intel Atom, ie low performance. While Atom's and AMD's equivalents have gotten better, they would probably still be a downgrade from your current system.

The main issue with a system move (beyond all the work involved with the transition) would be how to handle the massive amount of storage you use. With the current Mac Mini, Firewire 800 would be the fastest external port for disks. A future Mini (likely to happen in the next 3 months) may add Thunderbolt, but accessories for the new connection are still rare right now. The Dell systems have external eSATA ports, so that might make more sense for your current needs.