This is about making EC, and Dil. Doing missions/STF's/whatever and getting drops, this is obvious and I'm not going to go over it. You do whatever, get a lucky drop, sell it.
The bulk of this is going to be about doffs, because I work the hell out of my doffs and you should too. But before that, how to earn your keep in star trek?
Dailies: There's a lot of daily for dil missions. You more or less have to figure out which ones you like. Here's a list which also tells you what they're worth: http://www.stowiki.org/Daily
Academy Event: This is decent dil, you can get over 2k/hour.
Mining: Dunno, I think this sucks. It's really not a lot of dil at all, even during the event. On the other hand, it doesn't take long.
STF's: Don't forget all your STF drops can be redeemed for dil, and you get about 500 for a normal and 1k for an elite, not counting drops.
Mirror Event: Every mirror event run is 480 dil, my personal record is running it 9 times in one hour for over 4k dil.
There's really not many ways too flat out earn EC's, other than getting good drops and selling them. The obvious exception is the tour the universe event. You fly around to different sectors and get flat cash rewards. With advanced engines, DI, RP, and all that jazz you can make over a million in an hour.
Now onto the real meat of this. First, let me say, if you're serious about making profit you need to get yourself some klingons. They simply put have an enormous economical advantage. It's all (mostly) about doffs. They get a lot more assignments that bring in wealth. All the ones that the feds have access to the klingons get (or, at least, an equivalent). However, the klingons get a bunch of their own as well.
Now to doffs.
First off, if you don't know, when you're on your doff screen if you click on the department heads tab it shows you your various departments. You can then click on the department to pull up a lot more doff assignments. It changes for each sector you visit, sometimes slightly and sometimes a great deal. The first officer section changes the most.
There's a "haggle for..." missions for every gamma quadrant commodity. They use any doff, but but traders and quartermasters work best. A normal result gets you 5 of the commodity, a crit gets you 10. You can use these commodities in other doff missions. Some award extra dil, some award extra commendation xp. You can also just sell the commodities, and they sell well. You can find these in any of the orange areas around DS9, including the colonization areas that branch off the main sectors. They're also available in space around DS9, and in station on DS9, and from the ferenghi trader NPC found in DS9.
There's a ton of missions to secure such-and-such prototype. There's one for each torpedo and energy weapon turret type. I used to think these were worthless, I was wrong. See there's another assignment: "Deliver Prototype Technology to Allies in Gamma Quadrant." This assignment requires 1 each of the prototype plans you acquire from the secure missions (or via the exchange). It awards 1k dil, 20 of one gamma quadrant commodity, 10 of another, and 5 of the rest. On a crit, the dil awards go up to 3 or 4k, which is just an immense award. I got it once and was happy the rest of the day.
Strange Alien Artifacts:
There's a 1/1 assignment called negotiate the delivery of rare commodities. By itself, it comprises the children's toys assignment chain. Once complete, there's a repeatable assignment that's the same, but they add the word additional. Completing these gives you "Strange Alien Artifact" which you can use in an engineering doff assignment, which turns it into a powered artifact, and that you can use to create an XII console. Or, you can sell it. The chances of it becoming a purple console that's actually useful are really slim, and the doffs to get crits on this assignment are very expensive. You can sell the artifact for about 800k, and do it once every few days. If you actually get a good purple console, that's of course worth way more.
You should be able to get 5 colonists a day. There's an assignment called resettle colonists and it gives you 5 colonists to use as you see fit. The easiest use of them is to use them on the relocate colonists missions. That mission costs 5 colonists and awards 500 dil.
The other option with them is the colonization chains, each colonization area (like delta volnis, rolar nebula, ect) has a 7 part assignment chain. Part 2 requires 3 colonists, part 3 requires 4. Both of these are "regular" doff assignments; there's no special reward but they cost you colonists anyway. Part 5 requires five colonists, but it awards 500 dil just like the normal relocate assignment. The remaining parts have no colonist costs. When you complete one of the chains you're awarded a unique blue doff. You also unlock a repeateable assignment.
As I just mentioned, the colonization chains gets you a blue doff. But it also unlocks a repeatable assignment. That assignment is called Support Colonization Effort for whatever area you're in. A normal success awards you with a refugee, which you can trade in via the asylum missions for a doff. A crit success still awards the refugee, but it also awards a unique purple doff. These missions are repeatable, you can get multiple copies of each of the purple doffs. They're bound, but some of them you may want multiple copies of. Or, while you can't trade/sell them, you can turn them in for other doffs. You can exchange them via the academy personnel officer for 3 blues, or you can use them for the officer exchange missions.
There's collection of 4-part assignments in the DS9 orange areas where you basically build up a consulate with one of the DS9/gamma area races. The fourth part of the assignment costs you a diplo or advisor doff. There's 4 versions, each a different race, for each faction. Once it's complete, you get a repeatable "officer exchange" assignment, which lets you trade in any non-civilian doff for a new doff of that race. If you match up the traits you usually come out ahead on the deal. It also lets you unload some of your bound doffs (not all of them, there seems to be several kinds of "bound" doffs).
This is straight forward, you do the chain and you get a purple advisor with telekinesis.
Another chain, this one more valuable. It unlocks a repeatable assignment that basically functions like a klingon raiding assignment: You get some random items, usually commodities and maybe some equipment, plus a couple pieces of contraband. This isn't a big deal to a klingon but it's a big help to federation types. On a crit, you get prisons. At least a blue dominion prisoner, possible additionally some white normal prisoners. You can use the white prisoners normally, the blue dominion prisoner has special assignments. You can turn it in for extra cxp (worthless), or gamma quadrant commodities, or a gamma-race doff. I think the doff's the best deal.
Ghosts of the Jem'Hadar:
Yet another chain, 10 parts this time. There's cool downs in between so this takes awhile. At the end, you get a unique purple doff, Gul Tain, who's a projectile weapons officer. It also unlocks a sanctuary to anti-dominion cardassians repeatable which awards further doffs on a crit.
There's chain, one for each faction, for the furry-race (caitian/faresan). At the end, you get a unique flight deck doff, and a repeatable assignment to get further furry flight deck doffs of assorted quality. Likely you don't need a bunch of flight deck doffs, but they can be traded in for others.
In addition, don't forget the academy doff assignments, plus the various asylum, cultural exchange, and similar assignments.
Klingon characters make fed characters look impoverished. You think I'm exaggerating but I'm really not. It all basically comes down to marauding assignments. If you're not aware, instead of a "diplomatic" commendation category, and associated assignments, klingons get "marauding." Most of them are raiding this, capturing that, blockading something else. There's a lot of them.
These award a lot of STUFF. Commodities, equipment, and most importantly: prisoners and contraband. The commodities and equipment you mostly just sell to a vendor. It's not a lot of income, but it's better than what a fed gets.
You should really do every raiding-type mission you can, it's truly the wait to profit. The contraband you can turn in for dil, and even if you have your klingon(s) supporting your fed character it's very likely you'll still have enough left over to sell. You shouldn't sell contraband for less than 40-42k each. Which doesn't seem like a lot, but it quickly adds up. I have three klingons, and I probably sell at least 20 contraband a day.
Prisoners = dil, basically. There's three ways to deal with them. You can go to the security officer, who you turn in your contraband to, and you can trade in 10 prisoners for 1k dil. This is pretty much the worst value, it's 100 dill/prisoner and it has a pretty high fail rate. I pretty much ignore this option.
Second option is "forced labor requisition." There's multiple version of this, and you can find it in Eta, psi canis, and regulus sectors. If it's not on the current sector tab it'll be under your military department head, you can have 2-3 versions of it in one sector. This trades in 4 prisoners for 500 dil, which is the best value.
Thirdly is forced labor camps. These are found in the colonization areas, either in your current sector tab or under your operations officer in your department heads tab. This assignment trades in 3 prisoners for 350 dil, and there's a version of it for each colonization area.
Finally, not for dil, but you can sell prisoners to the orion slavers for latinum. You can also buy prisoners from them.
Between them, you shouldn't have any trouble unloading all the prisoners you can get your hands on.
Executing your way to riches:
Another fun klingon thing. There's a few assignments where you off a doff and get dill. They are:
1. Execute for Incompetence
2. Permit Crippled Warrior to Perform the Hegh'bat
3. Execute Mutineers
4. Execute Changeling Spy
1. is pretty worthless, I wouldn't even bother. It's just 5 dil. 2. is 100 dil, so that's definitely worth it to unload a white doff. 3 kills off 5 doffs, and you get 750 dil. 4. is the only one that might fail, but it only takes on doff and you get 500 dil on a success.
I know some of you are probably thinking why would you ever kill off your doffs... But here's the big secret: You can kill off your emergency holgram doffs. That's right, you can make an emergency medical hologram for 1k or 10k, then execute it as a changeling spy for 500 dil. Just like that.
More interested now? Thought so. 1, 2, and 3 are found in your personal section of doff assignments (as opposed to current sector). 4 will generally be found under the espionage category, so under your tactical or security department heads.
OK, that's all I've got for now. There's probably stuff I forgot or don't know about, so if you have any more such tips do please add them!