I actually used to work as a web developer for a guy who used to auction off liquidated office equipment.
What I did was set up his own company website for him that included an auction module similar to ebay's.
The auction module I used was from auctionanything.com but shop around. If this sounds interesting, try "auction module" as a google search and see what you can find. The guy I worked for said this worked much better than ebay for him because there was no competition.
The only catch though is that unlike with ebay, where people from all over the world already know about that site, you will have to advertise like crazy, especially in your local area, to bring in the bidders. If you don't advertise enough and only bring in 1 or 2 bidders per item, you won't make much at all.
Your best bet actually, may be to experiment a little. Try ebay first, since it's the quickest and easiest. If you don't find that you're making enough money that way, try the way I suggested.
If you do decide to go through with an auction on your own company site and you need help, email me at
ryan@yottasoftwaresolutions.com and I'll be happy to help.
good luck.