For romulan, I started out doing the two new queued romulan missions. The vault and azure nebula things. They were a quick solution to get me started on the rep projects since I didn't have to chase anything down, just queue up. I wasn't wholly satisfied with them though. They have both have timers before you can start, the vault one being kind of excessively long. And they both pay out on a scale depending on how successful you are. The azure nebula one is kind of annoying in that it's partly dependent on which trapped ships spawn, if you just get escorts and bops it's not going to add up to as many points. On the plus side, they both gave a small amount of fleet marks.
Since then I started doing the patrol missions and the tholian red alert. You can get both by clicking on a box when you zone into tau sector. The tholian red alert is hit or miss, it's like the borg red alerts in that you have to wait for it to spawn. It's also moderately tough. A lot more chaotic than the borg red alerts, and tholians are annoying buggers with all kinds of crowd control and the like. But you get like 15 romulan marks for completing it, then 30 more plus 480 dil when you turn in the mission. Not bad at all.
The patrol thing is a bit different. You accept the mission and you get thing in your quest sidebar that shows percent completed. You then fly around to different planets in the sector and Do Stuff. The pure combat planets give 20% each, the tholian red alert is 25%, and the non-combat or partial-combat planets seem to be 15% each. Do whatever sort you like the best. If you're looking to just get it done as quickly and with as little effort as possible: go the Acamer system. Here you fly to meet a frigate, then make a left and fly to meet some more ships. Then you click through some dialog. Pick the responses that seem reasonable/understanding, and then you're done. If you see a response that has [Diplomacy] or [Marauding] in it, that usually ends the encounter right there. If you flub the dialog you have to fight three waves of ships.
Any of the planets, including the acamer one, can be done over and over again. You can do one planet as many times as necessary to get 100% completion. Once you're at 100% you turn in the mission and get 60 marks.
For omega marks (Borg Bucks™), I've done some of the borg red alerts. They give 10-15 marks and 480 dil. But mostly, I've just been doing STF's.
I just do infected space elite. It gives 60 Borg Bucks™ a neural processor and 960 dil, plus 15 more Borg Bucks™ if you get the optional. The rest I can't be bothered with anymore. You no longer need specific tech drops, ground STF's are generally a pain, and the other space STF's have failure conditions. Someone pops a cube early? Or completely ignores the probes or birds of prey? Chances are it's game over. But infected doesn't have a you-lose trigger, so even if someone does something bone-headed you can usually still finish and get your reward.