If you have any two of the three Ferengi items from the Lobi Store (Missile Launcher, Mine Layer and Rule 64 Console) it takes another 20% off the prices from space-sector cargo vendors. 20% may not sound like much, but when you are buying 5000 Industrial Doohickeys, it certainly saves a lot of EC! You can even just keep the items in your inventory and only slot them in place when you want to talk to a cargo ship. I fly with the console and missiles anyway, so I've always got the discount.

I believe Ferengi characters get deals at the vendors as well, don't they?

Yes, the "Lobes" discount is 20% off from commodity vendors on starbases. However, can't play a Ferengi on the KDF side.

I have had the problem of the original poster, however, the cheapest way for me is to buy them on Fed side (w/my Ferengi, of course) and mail them to my other characters. A pain with things like large hypos and major regenerators, but still worth the time and hassle.

valiant797's post (see his post earlier in the thread) is the best for finding where the cheapest vendors are located, and the Ferengi discount also applies on top of the discount vendors, if you happen to have a Ferengi character.

Use the Call Tuffli channel, a fair few frieghter captains listen to it. If you are polite you could likely get an invite fairly easily.

STOWiki has a nice article on Commodities. There's a "Strategy" section at the bottom of the page that lists the best places to buy for both Federation and KDF.

As far as the cost, I find that when I do the Tau Dewa Sector patrol daily mission, I usually pick up enough loot to sell to cover the costs of buying commodities for both Romulan and Omega Force reputation assigments. I've been mostly doing this with my main Federation character, but I would think the same would apply to KDF.