This analysis is server specific to Antonidas (US) and may not match what's happening on your server though I do believe the epic gem market is following a similar pattern on most servers.
Prior to patch 4.3 I made some educated guesses and came up with the following:
What I expected
I figured epic gems would start out insanely high priced (20k+ per gem for reds, 10k+ for other colors) and virtually none would sell at those prices. I also thought it would be possible to pick up the occasional far more reasonably priced gem out of trade chat, especially after someone spent a day or two *not selling his precious red gold mine at the crazy initial prices everyone would be asking.
For the short term (the first month or so) I decided 4-5k would be a good price to buy red epic gems at and 2-3k for other colors. The plan was to buy raw gems at those prices, then cut and resell them for a 1-2k profit (maybe even more for the first few of each color).
Over the middle term I figured red epic gems would go for around 4k raw and 5-6k cut. The other colors about 1.5-2k raw and 2-3k cut. I felt this would continue until several guilds have been farming most of the new bosses for a while, upgraded most of their gear, gemmed it with epic gems and began getting more epic gems than they use. It's hard to predict how long this phase will last, it could be just a month or so or it could last for several months.
For the long term I expected red epic gems would eventually drop to around 2k raw, 3k cut and other colors to 1k raw, 1.5-2k cut. This could take several months, particularly for red gems. Other colors will almost certainly drop in price sooner and possibly much sooner than red.
Of course there are other factors that could affect the market by increasing the availability of epic gems. For example the possible future addition of transmutes, prospecting, vendors or any other new source of gems could cause prices to drop further and faster.
Then the patch finally landed....
What actually happened
As expected the price of the first few gems posted on the auction were outrageous. The first Queen's Garnet (red) was posted for 25k. Naturally the sheep (or lemmings) followed by posting at prices like 24,999g. Around 24 hours later someone finally posted one for 24k. Non reds were posted for 10k+ and most more like 20k.
I started out barking trade to buy red gems for 4k and other colors for 2k. I got a couple non reds for 2k and that was it. No reds at all, everyone thought they could get 20k+ because "4k? LAWL! They're going for 25k on the auction!". Another player was spamming trade constantly for reds, offering 3k at first, then 4k when he noticed that's what I was offering.
After a couple days I'd only gotten 1 or 2 more gems and still no reds so I bumped my buy prices to 5k for reds and 2.5k for the other colors. I got my first red gem that night and started getting a few more of the other colors though I paid 3k for the very first of most colors.
I posted my first red gem for 10k raw and the other colors for 6-7k. Intentionally higher than I thought they'd sell for but not insanely high like everyone else. I wasn't expecting many (if any) to sell. All I wanted to accomplish with the first few gems was to stabilize the market and educate people that 10k+ prices were not just unrealistic but completely unreasonable.
Over the next couple days I picked up a few more gems. Whenever I got a 2nd gem of a particular non red color I'd cut the most popular cut for that color and post it for 7k. Purified, Reckless, Puissant, Fractured, etc.. I got a couple more red gems and hung onto them raw, just posting one for 10k since everyone else was still posting red for 20k+.
Then, someone bought my raw red gem for 10k and re-posted it for 16k. I posted another for 10k. He bought that one out the next day too and posted 2 for 13k each. I posted another for 10k. 12 hours later he posted both of his for 12k each. The next day he was posting them a little under 10k, less than he'd bought them from me at in the first place.
I sold a few non red cut gems for 5-7k too, about 1 a day or every other day while slowly building up a small inventory of gems. Most days I got enough raw gems to replenish stock as it sold and get 1 or 2 new cuts posted. I picked up a few more red gems for 5k each, cut 1 each of bold, brilliant, delicate posted them for 7500k and started dropping my maximum prices on the other 5 colors by 500g per day.
Over the next few days I sold 1 cut red gem and a few more of the other colors. I dropped my maximum selling prices for reds to 7k, other colors to 4.5k and my buy prices to 4k and 2k respectively. Two of my cut reds sold for 7k the next day so I raised my maximum sale price on them back to 7.5k. Nobody is undercutting me on red gems yet, or if they have, their's sold before I noticed them. I sold several more of the other colors too, mostly in the 3-4k range and 2 or 3 for 4.5+.
That's where things are sitting now. I didn't manage to buy any more reds for 4k and very few of the other colors for 2k yet. Today I started offering 5k for reds again but I'm sticking with 2k for the other colors. Selling prices I'm sticking with 7.5k for reds and down to 4.25k max for non reds.
I'll probably drop my maximum sale price for non reds to 4k tomorrow and depending on how buying more works out, 3.5k or even 3k within a week. For red gems a 5k buy price and 7.5k sell price seems to be the sweet spot so I think I'll stick with those prices until I start seeing them cheaper than that on the AH.
I expect reds will stay at 5k raw and 5-7k cut for quite a while yet. No doubt many will be posted even higher but I don't think they'll sell very well. Mine sold very slowly at 7.5k anyhow and that was with almost no competition. Demand for red gems should continue to grow as more guilds progress further and get new gear that needs gems. As guilds start doing heroic modes and getting BiS gear demand will grow even more. I don't see red prices dropping significantly until several guilds are far enough along on progression and farming to be producing surplus red gems beyond what they need for themselves.
Non red gems I expect to continue slowly spiraling downward in price until they're around 1k raw and 2k cut. Lava Coral and Shadow Spinel will likely fall faster than the others. The reason being those gems are available in greater supply since they both (and Queen's Garnet too) drop from Elementium-Coated Geode while the other 3 do not. This is already starting to happen especially with Shadow Spinel which doesn't have as many good cuts as Lava Coral. Lightstone, Deepholm Iolite and even Elven Peridot are usually 3-5k uncut on the auction, Shadow Spinel 2.5k - 4k and Lava Coral anywhere from 2.5k to 5k.