Here is a list of acronyms and other terms that are frequently used.  Thanks 
to
all who have helped me create this list!
Star Trek acronyms
==================
     Shows and Movies
     ================
TOS     - The Original Series                    AGT    - All Good Things
TAS     - The Animated Series                    BOBWI  - Best of Both Worlds 
I
TNG     - The Next Generation                    BOBWII - Best of Both
DSN/DS9 - Deep Space Nine                                 Worlds II
VOY     - Voyager                                EaF    - Encounter At 
Farpoint
TMS     - The Movie Series                       RI     - Redemption I
TMP   - The Motion Picture       (Star Trek I  ) RII    - Redemption II
TWOK  - The Wrath of Khan        (Star Trek II ) UI     - Unification I
TSFS  - The Search for Spock     (Star Trek III) UII    - Unification II
TVH   - The Voyage Home          (Star Trek IV ) ITHOTP - In The Hands Of The
TFF   - The Final Frontier       (Star Trek V  )          Prophets
TUC   - The Undiscovered Country (Star Trek VI ) IWWH   - If Wishes Were 
Horses
GEN   - Generations            (Star Trek "VII") RoA    - Rules of 
cquisition
FC    - First Contact         (Star Trek "VIII") WNOHGB - Where No One
WNMHGB  - Where No Man Has Gone Before (TOS)              Has Gone Before 
(TNG)
     Others
     ======
BoP   - Bird of Prey                  PHASER   - PHASed Energy Retification
E     - Enterprise (EA=1701-A, etc.)  RETCON   - Retroactive Continuity
Ex    - Excelsior                     RHT      - Rerun Hell Time
FASA  - Freedonian Aeronautics and    ROTBA    - Reality On The Blink Again
        Space Administration (Role    RPG      - Role Playing Game
        playing game company that     SD       - StarDate
        used to publish a Star Trek   SFA      - Star Fleet Academy
        RPG)                          SFX      - Sound Effect(s)
FTL   - Faster Than Light             TGBOTG   - The Great Bird Of The Galaxy
FX    - Special Effect(s)                        (Gene Roddenberry)
GNDN  - Goes Nowhere, Does Nothing    TMOST    - "The Making of Star Trek"
GPL   - Gold Pressed Latinum          TNGTM    - TNG Technical Manual
GR    - Gene Roddenberry              TNZ      - The Neutral Zone
IDIC  - Infinite Diversity in         TPI      - Tuvok Pip Issue
        Infinite Combinations         TPTB     - The Powers That Be
IMOGR - In Memory Of Gene Roddenberry UFP      - United Federation of Planets
JAG   - Judge Advocate General        USS      - United Space (Star) Ship
LASER - Light Amplification by        VISOR    - Visual Instrument and
        Stimulated Emission of                   Sensory Organ Replacement
        Radiation                     VHTSKOOI - Voyager Has The Snot Kicked
LLaP  - Live Long and Prosper                    Out Of It
NASA  - National Aeronautics and      WF       - Warp Factor
        Space Administration          YAGLA    - Yet Another God Like Alien
NCC   - Naval Construction Contract   YAOI     - Yet Another Odo 
nconsistency
        or Navigational Contact Code  YATA     - Yet Another Transporter
NX    - eXperimental Registry                    Ability
OPI   - O'Brien Pip Issue             YATI     - Yet Another Trek
PADD  - Personal Access Display                  Inconsistency
        Device                        YMBAT    - You Might be a Trekkie
PaLL  - Peace and Long Life                      (Trekker)
     Common Terms
     ============
CANON   - what Roddenberry/Paramount decided/decides is "official" Trek.
SPOILER - Discussions of shows/movies that would "ruin the plot" for some.
TEASER  - The part of the episode before the opening credits.
TRAILER - A preview or commercial for an upcoming episode.
     Universal Acronyms and Symbols
     ==============================
AFAIK       - As Far As I Know              GMTA   - Great Minds Think Alike
AAMOF       - As A Matter of Fact           IIRC   - If I Remember (or 
ecall)
AAMOT       - After A Moment Of Thought              Correctly
AWGTHTGTATA - Are We Going To Have To Go    IMHO   - In My Humble Opinion
              Through All That Again        IMNSHO - In My Not So Humble 
Opinion
BSG         - Big, Silly Grin               IMO    - In My Opinion
BTW         - By The Way                    L8R    - Later
c           - speed of light (physics)      LOL    - Laughing Out Loud
              186,000 miles per second      OOTC   - Obligatory On Topic 
Comment
              [300,000 kilometres per       OTB    - Off To Bed
              second or 3 x 10^8            OTOH   - On The Other Hand
              metres/second]                POV    - Point of View
EOT         - End Of Thread                 ROTFL  - Rolling On The Floor
ETC         - Et Cetera                              Laughing (Many 
Variations)
FAQ         - Frequently Asked Question(s)  TIC    - Tongue In Cheek
FWIW        - For What Its Worth            TTFN   - Ta Ta For Now
FYI         - For Your Information          TTYL   - Talk (or Type) To You 
Later

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