I'm a professional disenchanter, and the following advise will probably cut into my profit, but I'm a bit tired of taking money off people that they can get for themselves.
I get most of my disenchanting material from the Auction House on bids. Many times, the bid prices are so low that I triple or even quadruple the money I spend on bids. I'm satisfied with doubling, and that excess money should go into the pockets of the person who put up the item.
OK, first of all, get enchantrix (part of the Auctioneer package). When you go into the auction house type to sell a green or better item, type in "/enchantrix load" this will allow you to display the price that disenchanted material sells for.
When you move your tooltip over something you want to put up for auction, enchantrix will display 3 prices for the disenchant material:
HSP - Highest sellable price
Median - Median price of the disenchant materials
Base - Base price of the disenchant materials
You can pretty much ignore the base price. Basically it's the price from Alla and probably won't apply to your realm. That leaves you with two prices. The HSP and the median. figure on using the HSP to determine what price to set your minimum bid at.
For example if Enchantrix displays the following:
HSP - 41s 20C
Median - 43s
Base - 20s
The minimum bid that you should set should be 1/2 the HSP. If Auctioneer also shows that the item will normally sell for less than this amount, then it should also be your buy-out price.
If you have a good Auctioneer database, Auctioneer may tell you that the minimum bid price should be higher. If it does, follow it's advise. It's generally good, and if I lose out on some disenchanting material, then "oh, well". I'll be able to find something to disenchant - don't worry. However, if Auctioneer tells you to put the minimum bid lower than 1/2 the Enchantrix HSP, then you need to raise that minimum in order to make a bit more money.
p.s. You can also use this advise for making money disenchanting - you can determine which items to buy on the AH to disenchant and at least double your money.