Jargon and slang

CE: Crystalline entity. This impossibly difficult PvE fleet action required and enormous amount of coordination and luck and requires 10 or more players who will listen and coordinate with each other to defeat it.
STF: Strategic task force. Refers to a series of challenging space and ground missions that require players to accomplish specific goals to complete the mission and get the reward. Often the names of STFs are shortened to acronyms which can be confusing the following explains them
First part - Name of the mission:
Infected = I
Cure = C
Khitomer accord = KA
Second part - Type:
Space = S
Ground = G
Last part - Difficulty:
Normal = N
Elite = E
Examples:
ISE = Infected Space Elite
ISN = Infected Space Normal
IGN = Infected Ground Normal
KAGE = Khitomer accord Ground Elite

Pub: Public match. Sometimes when there aren't enough ponies to play with you have to Queue for the public fleet actions. Players dislike doing this as more often than not you end up with one or more pubbies or pubs on the team

Pubbies/Pubs: These are players who make a fleet action (usually an STF) more difficult. Usually this is because they haven't the faintest clue as to how to go about doing said fleet action. More often than not this includes, not paying attention to team chat, blowing up things when they are not supposed to, or pestering everypony in the team with questions of what they are supposed to do. Contrary to popular belief pubbies are less common in elite STFs as more often than not people playing those missions have some idea of how to play the mission.

Boffs: Bridge officers.
Doffs: Duty officers

It took me ages to work out what boffs and doffs meant, and i didnt want to ask in case i looked dumb
Thanks for the list!

And to add to the list:

Dil: Dilithium
Excel Retro: Excelsior Retrofit Cruiser
EDC: Encrypted Data Chip
EC: Energy Credits
GPL: Gold Pressed Latinum
STF: Special Task Force(the Borg PvE missions)

Simple acronyms
ESD: Earth Space Dock
DS9: Deep Space Nine
MVAE: Multi-Vector Advanced Escort
Ody: Odyssey

Gekli: Fluidic fleet action. This is yet another early and badly thought out PvE mission. It involves herding gekli towards a specific area on the map. The problem is that the gekli often go in a different direction than what you want them to. Making the mission boring and a complete pain to finish. It is also very buggy and nearly impossible to complete.
Science: Sometimes this term is used to refer to casual PvP matches between various fleet members to test the strength of an experimental ship build they have come up with.

Celestia wrote:Science: Sometimes this term is used to refer to casual PvP matches between various fleet members to test the strength of an experimental ship build they have come up with.

The term "Science" is also applied to a full team of Science captains running through missions and other events. Please note that said term cannot be applied to teams that are not completely comprised of Science captains.