So, I transferred my main over to see what effect it would have on the character. Here's what I noticed happened:

First the money part. As far as I can tell, EC and GPL were unaffected by the transfer (no shock there).

Pre-transfer I had the following:
Marks - Exploration 17, Valor, 2, Excellence 94, Distinction 25, Bravery 36
Badges - Fifth order 150, Third 32, Second 75, and First 35
Emblems 241

Post transfer: 97,262 refined dilithium (that's REFINED)

Now in the C-Store it gets a little weird. I had already bought Excelsior and Nebula pre-transfer. My nebula that I fly was converted to the new +1 version (sweet, I can swap out the Tachyon Grid!). I also had "purchased" the Intrepid Retrofit with my VA token. All three ships were available to me without any problems (though I had previously claimed all three with this character).

Problem 1: I no longer have access to the T3 versions of the (C-Store) ships. Since seperating them, apparently I'm not cool enough to have both (even though that is what I purchased)

Problem 2: All my bridge packs have disappeared. The C-store (and ship editor) makes it appear that I have to rebuy all of them. Funny quirk, if I beam to my bridge, it's still my purchased one.

Problem 3: My purchased clothing items are gone as well. The one I know for sure is the open jackets, which is no longer an option. Again, my BOff who is currently wearing it still it, but if I try to select it on any new ones, it asks for money.

Problem 4: Ship costumes are missing. Apparently it's all the vanity items that are gone.

That's all I've noticed so far. Feel free to post any other things you've noticed in conversion or if your items are missing as well.

So based on your math they are weighing emblems way higher than the other currencies. You should see my post on a buying analysis. These formulas are way way off.

C-Store purchases are not transferring over on purpose. They have spoke at large on that subject.

I had about 2000 Exploration badges and now I have about ~57,000 dilithium.

1,353,055 merits
5,025 emblems
1,032 marks (combined Exploration, Honor, Valor)
5,310 medals (all 5th order)
66,123 badges (combined 1st-5th)

=> 1,329,529 refined and 384,000 ore

It appears that no one has gotten more than 384,000 ore after transferring a character from Holodeck.

12 Nov Edit - For those who may want to use my data for currency conversion calculations:
1032 Mark breakdown: 930 Exploration, 67 Honor, 35 Valor
5310 Medal breakdown: 5310 Excellence, 0 Distinction, 0 Commendation, 0 Bravery, 0 Achievement
66123 Badges breakdown: 23545 5th, 10443 4th, 10571 3rd, 10646 2nd, 10918 1st

Can I get a screen shot? 1.3 mil merits seems outrageous to me. (not calling you a liar tho)

1.3 is not unreasonable... Playing since headstart, having completed all new content fairly fast, leveld to cap fast... Trust me... it will give you MORE than enough time to accumulate that amount. and then some if you don't respec often.

I bet PH has thrown away more emblems than most of us ever acquire.

Really? I would. 5k emblems? I call that unlikely.

Screenshot posted here and was done as of 6:11pm CST on October 19, 2011.

I play pretty much every day and would often earn over 20 emblems a day by doing most/all of the dailies, up until the last few months. If there's any lingering doubt, feel free to ask the people on Accolades as I'm a regular there.

Apparently I attract Commodores to my posts

I didn't feel like doing any math, but I put the numbers up for those who are interested.

And apparently they are allowing c-store purchases to come over, if those c-store purchases are ships. What I find interesting is that the things that I've already purchased, claimed, and unlocked are effectively relocked. I wouldn't have a problem if I couldn't claim them on new characters on Tribble, but it's kinda weird to not have access to them on the transfer character. It doesn't affect anything, so I'm not shedding any major tears about it.