Nightmare's Notes
These are some tips to make things go smooooothly.
Safe Shipping
Make sure you get their name, street address, and even a phone number if you can! Don't settle for a P.O. Box address, there are ways people can commit fraud with those so don't trust them. If they don't want to give you their name then obviously something is screwy. Also, always use Delivery Confirmation. It costs about 75 cents now, this lets you track a package from the moment you ship it to the moment they receive it, this way they can't cheat you by saying they never got the package. You can also buy Insurance or require a Signature from them before the package is given to them.
Communication is Important!
Decide on exactly what you both want at the very beginning of the deal so there are no arguments later on price or time or whatever. Request work-in-progress pictures to see if you want anything changed along the way. Ask if they need anything or if everything is going just fine. Remember, you're both depending on each other uphold your part of the deal, be active, ask questions, have them feel secure that you're actually going to pay for the custom when it's done. But don't be afraid to call them out on something if they aren't doing what you agreed on. Don't be rude of course, but if they don't do what they promised then request a discount, ask for a bonus item, maybe ask them to reimburse you any shipping charges, don't just keep quiet! Instead of sending them an email, make a public post in their topic (if they have one) and just ask outright why they aren't done yet, or whatever the case may be. People get their shit straight when their reputation and business is at stake.
Trust
If you have trust-issues then don't get into this in the first place. You have to have trust in the person you hire, don't be pecking at them for receipts and exact costs of materials, that's a huge annoyance, it'll put any customizer in a foul mood. Like I said, this guide is here so you won't get "ripped-off", I'm going to give you the average costs of all the materials I can think of that go into making a custom. I'm a customizer, I know what this stuff costs, and you can either trust me or do the research yourself. 
Costs
Use this info to guesstimate how much a commission will cost in materials. Keep in-mind that in addition to these costs, the customizer is also going to charge you what they think their time and talent is worth. Also remember to factor-in shipping costs which can get very expensive, especially if the customizer is in another country. Try to be as efficient as possible, send everything the customizer asks for in one package.
The following are the common price-ranges for the materials used most often. All prices are in U.S. Dollars:
Paint: $2.00 - $4.00 per bottle; Sealer: $2.00 - $5.00
Quality paint is expensive and worth the price for a great paint-job. Nothing ruins a custom like crappy paint that clumps all over. Odds are that the customizer already has the paint needed for your custom, but sometimes they have to buy a certain color for it or they simply run-out of a needed color. Sealer is used to protect the paint from rubbing-off.
Sculpting Material: $0.00 - $30.00
This is going to vary tremendously depending on how much modification the custom needs. Most people aren't going to charge you for every little gram used, but if the custom requires a lot of sculpting (like armor) then be ready to pay a little more. $25.00 is an extreme though, with that money we can buy enough sculpting material to last a dozen customs, give or take a few.
Base Figures (Fodder): $?.??
Sometimes customs have cost me only $5.00 to make, sometimes $30.00, it depends on how many figures you want to buy and what parts the customizer has in their Fodder Bin (extra parts bin, they all have one!). A "Marvel Legends" figure costs $5.00 to $15.00, if you need 3 figures to make the custom, then the figures' cost will be $15.00 to $45.00 (3 x $5.00; 3 x $15.00). Look for discounts and sales whenever possible! Remember to discuss who gets to keep any left-over parts from the figure or Build-A-Figure pieces or any accessories (guns, flames, armor, whatever).
Miscellaneous: ?.??
Customizers use all sorts of junk to make customs! Cardboard, Q-tips, foam, hot-glue, toothpicks, paperclips, fabric, rubber-bands, plastic-wrap, whatever gets the job done! Though I really don't think they should charge you for Q-tips or plastic-wrap, they have a right to do so, everything costs them money after all.
Real World Examples
Here are two perfectly plausible commissions of well-known characters to give you an idea of total costs for a commission. Remember, prices will always vary depending on many variables like size, detail, mood, alignment of the moon and stars...you get the point. Click on the figure's name to see an example of a custom of it.
Custom Symbiote Spiderman (6 Inch)
This shouldn't cost more than around $20.00. Seriously. You've seen this suit, it's all black with a white spider-symbol, like Venom. All you need is a plain base-figure, black and white paint, and maybe some tape to help paint the symbol straightly. Let's say you want them to use a Marvel Legends Bullseye with a few modifications (different limbs), this is pretty simple:
Let's tally some costs:
Figure: $7.00 (you find it at a flea market and you have the other pieces to complete it)
Paint (x2): $6.00 (B&W paint, you might not have to pay for this if they have the paint)
Shipping: Depends where you are and what method you use (Post Office, UPS, etc.), around $3 to $15. Remember, someone has to pay to send the custom back to you.
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Total: $16.00 ($7 + $6 + $3 shipping)
$16.00 is the cost of materials, this is the ideal cost, but shipping will vary and no one does anything for free! The customizer is going to charge you for their time and talent (Labor Fee), obviously it's going to vary greatly. What's it worth to you? If they say $20.00, then the custom is going to cost you $16.00 plus $20.00 in labor, so $36.00 total, about $40.00 if you pay the shipping back to you. The customizer only got $20.00 but you paid almost double because of materials.
That's just for a repaint, imagine if you wanted some crazy complicated character made? Let's take a look at the potential cost of that behemoth.
Custom Iceman - Age of Apocalypse (12 Inch)
Obviously a 12-inch figure is going to be a heavy load, let's be optimistic and say $12.00 shipping total. The base figure used here was a 12-inch Human Torch, which is around $20-$25, give or take because of tax. To achieve the "ice effect", many customizers use a wide variety of pearl and/or metallic paints, usually stuff they don't have just lying around. Again, let's be optimistic and say it'll be like $10.00 for paint, a 12-inch figure has a lot of surface to cover, 10 dollars for paint is a steal. Also, you're going to want those cool jagged ice pieces AoA Iceman has all over his body, that takes sculpting material and/or foam/plastic/glass/glue, let's say another $25.00 for those materials. Now the Labor Fee comes into play, let's say the customizer is a cool dude so he'll do it for $50.00.
Let's tally the costs:
Figure: $25.00
Paint: $10.00
Extra Materials: $25.00
Labor Fee: $50.00
Shipping: $12.00
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Total: $122.00
That's a lot of money, but the customizer only gets $50.00, maybe even less if they have to pay the gas for the car to go buy the materials at the store or pay to have the store ship it out to them. Remember, the customizer isn't making a lot of money on this deal. If it takes them a day to finish the custom then they just got $50.00 for 24 hours of work, that's not very time/cost effective is it? This is truly a labor of love.