Hi! I'm Aeren@Dark83 in STO, and I've heard some basic quesitons about reputation being asked recently, so I thought I'd make a quick introduction.
Welcome to level 50!
You've unlocked the reputation system, congratulations! You should start on it immediately.
What about missions, the foundry, or PvP? No. Reputation system. Now.
Why now?
The reputation system is time gated.
Every reputation system has a 20 hour project (which gives 2500xp) you can do once a day, and a 1 hour project (which gives 200xp) you can do three times a day. Those are the only ways to advance your reputation, which means there is a minimum amount of time necessary to reach Tier 5 - 40 days. No amount of additional effort will cut the time required, your progress is capped - so start ASAP!
Which One?
All of them. At the same time.
As mentioned in the above section, you can't focus and grind any particular reputation system. The progress you can make is limited, so you may as well do all of them at the same time, and it's not even going to take that much time.
Each day, the first time you do a mission related to a specific reputation system, you are rewarded a bonus of 50 relevant marks. The 20hr project requires 30 marks, and the hourly projects require 20 marks. That means doing one relevant mission a day will give you enough marks for the daily and one hourly from just the bonus alone.
Taking one point in the Undine space battle zone counts, doing the random mission offered by Joint Command in the Dyson Sphere space counts, one mission in Nukara counts, and so on. It doesn't take much time or effort, just 5 missions spread amongst different content.
If you don't do all of them at once, and instead you do 5 missions for a specific reputation system, you're going to be short 200 various marks a day. Overall, you'd need to put in ten times as much time/effort to work on just one reputation system at a time, and you won't be advancing them any faster. Ten times the effort for quintuple the time? Doesn't sound smart to me!
Easy Romulan Marks
Romulan Marks have an extra method to attain which is unique to it - Epohh Tagging.
Spend a few minutes a day tagging Epohhs, and you'll have 4 Active Tags each day. 4 Active Tags are used in a daily DOff assignment, which gives 1 Epohh Research on a Success, 3 on a Critical Success. You should hopefully be able to get a Critical Success at least 25% of the time (there's a Very Rare Paradan Astrometic Scientist that will put it to 26%), which means around 6 Epohh Research every 4 days, 30 Epohh Research every 20 days.
If you have 5 Epohh Research, you can buy an Epohh pup. So 6 Epohh pups every 20 days. It's a 1 day assignment to raise a pup to a moppet, a moppet to an adult, and then an adult to an elder. So after a 3 day delay, you should have 6 Epohh elders every 20 days. An Epohh elder can be cashed in for 400 Romulan marks - which means 2400 Romulan Marks every 20 days.
Not bad for a few minutes spent tagging Epohhs each day! It's the best possible effort:reward ratio of all the reputation systems. If you do this when you start working on Romulan reputation, you should easily have enough Marks to buy anything you could possibly want from the Romulan reputation system by the time you hit Tier 5.
Events!
The critters we can raise in the summer and winter events (birds, monkeys, candy epohhs) are basically like this, but can be cashed in for any type of reputation marks. Handy!
Easy Omega Marks
The Borg reputation is rather unique in how easy it is to grind, because of eSTFs. eSTFs stand for Special Task Force missions on elite difficulty. At this point in the game they're trivial for most of us veterans, and the space ones are popular. Just ask for ISE (Infected: The Conduit, Space, Elite), CSE (The Cure Found, Space, Elite), or KSE (Khitomer Vortex) on our {UFP-UFPK} channel and you're likely to be able to get a quick team that can massacre the Borg. It's an easy way to get your Omega Mark daily, as well as get the widgets for Omega Reputation gear.
Closing Statement
Hopefully I didn't waste your time and you learned something useful.
Remember, I'm pulling for you, we're all in this together! If I made a mistake, don't hesitate to correct me.