As you all might know, the only way to trade or transfer items between Horde and Alliance is via the Gadgetzan auction house in Tanaris. Here is my question:

I want the Elite Mount for my Night Elf Druid, but have collected 1000 gold on the Horde side. Transferring the money is simple: My Night Elf puts a piece of Woolen Cloth for 1000 gold in the auction house and my friend on the Horde side, whom I gave the 1000 gold first, simply buys that piece of Woolen Cloth for 1000 gold. Sounds easy, but there is a catch: Recently, we have transferred just 20 gold this way to my Night Elf and she got just 17 gold or so back from the original 20 gold buyout for the piece of Woolen Cloth. So, there is obvioulsy a huge auction fee on such deals (in Gadgetzan).

Does anyone know how high that fee is (in perecent) and how much of the 1000 gold I would lose? Also, is there a procedure/trick to keep that fee as low as possible, or avoid it at all (in Gadgetzan)?

Not to game the system, but the AH prices are based on vendor buy/sell prices. If you find something worthless to vendors it will cost nothing to put at the AH.

Pretty sure there is also a percentage-based commission, This is like 5-10% for the faction AHs, but about 20% for the Gadgetzan AH. So, say you auction something for 20g that has a 1g auction deposit fee, and it sells at buyout price - you get back 20g - 1g (the commission) + 1g (the deposit fee) = 20g. Contrariwise, if it doesn't sell, you're out the deposit fee period.

So, would a Power Crystal from Un'Goro, for example, give the full 1000 gold back to my Night Elf if she puts it for 1000 gold buyout in the auction house and my Horde friend buys it?

An alternative way to do this is to buy some epic items Horde-side, transfer them for 1 silver buyouts, and then sell them Alliance-side. There is naturally some risk involved, but you will avoid losing the percentage-based fees.

*lurks in waiting at the Gadgetzan AH to snipe the itamz*

I did this before, but it's to much hassle IMO

No. The vendor price is used for determining the deposit you pay when placing the item for auction (IIRC 5% for an 8 hour auction and 15% for a 24 hour) so there would be no deposit on a power crystal which has no vendor price. There is then the actual commission they charge based on the sale price. So, if the item sells, the money back to the seller is (sale price - commission + deposit). Of course, if the item doesn't sell, you get the item back but lose the deposit. That commission is 5% in the main alliance and horde auction houses. I thought it was 30% in the Gadgetzan AH, but that would be wrong if 17 was returned on a 20 sale.

Is there any reason why it's so high in Gadgetzan? Perhaps to make money transfers, like the one I have in mind, unattractive?

Indeed, this is so high to prevent money transfers. The fee is 15%. as Xanthix said, the best way to transfer money is to transfer items. Check the prices from both AH, there are some items that have different prices depending the faction.
In my server for example the arcane crystals cost more horde side than alliance, so if you want to transfer from alliance to horde, you just buy the crystals and transfer them for 1s, thus almost no fee paid. then sell them horde side cheap and get the money you invested back, with maybe some win.

Well, 15% would mean that I loose 150 gold of 1000 gold if I transfer the money via a piece of Woolen Cloth to my Night Elf. On the other hand, I have the cash now, not the Arcanite bars anymore, so I'll collect 5 crystals more and pay the fee, I guess

In any AH transaction, you're going to lose that money.

One way to transfer it would be to post on the forums and see if you can work out a deal with someone. 1000g Horde for 1000g Alliance. There maybe someone in the same boat as you, looking to transfer money to their Horde alt.

I placed a shield for 70g from my alliance char and got my friend to buy it Horde side for me , I got a return of 60g and 37s almost 10g went to the AH . I once sold something for 350g I think but not exactly sure but it took around 40g .

I believe the Gadgetzan AH commission is 15%. However, they factor it in with the deposit you pay.

So on a particular item let's say deposit fee is 35g and it sells for 1000g buyout. The seller would end up getting 885g in the mail. Counting the 35g deposit paid, the seller actually came up 850g, or 85% of 1000g.

This is also why sometimes you get back more money in the mail for a sold buyout auction then the buyout price; the initial deposit fee itself was greater than the amount of commission.