Array= Buffet
Barclay= Brownoserly
B'Elanna Torres= Batonna Torcheress
Bothans= No-ah-face-ah
Cardassian= Cardashboardian
Caretaker, the= Genetaker
Carey= Corny
Caylem= Crazem
Chakotay= Chuck-up-tay
Crosby= Crotchety
Crusher= Crutcher
Culluh= Cola
Data= DooDah
DeLaney= DaLoony
Doctor, the= Doctor Who
Dukat= Doggy-dooky
Earhart= Airhead
Enterprise= Doorprize
Federation= Flatulation
Freya= Laya
Haakonian= Hedonian
Jetrel= Intel
Kazon= Clap-on
Kes= Kiss
Kim= Prim
Kira= Kleara
Kirk= Smirk
Klingon= Kluckon
Kolopak= Cola-pack
Libby= Del-Monte
Lieutenant= Lietenant
Maje= Mangy
Maquis= Ma-Sleeze
Metreon Cascade= Mets Cascade
Mokra= Ocra
Nacene= Napalm
Neelix= Buttlix
Ocampa= Summercampa
Ogla= Oogly
Paris= Pompous
Phage, the= Pizzaface
Picard= Pick-Hard
Riker= Piker
Sandrine= Latrine
Seska= Freshka or Bitchka
Spock= Spook
Starfleet= Star Fart
Star Trek= Star Farce
Sulu= Sulo
Suspiria= Suspicion
Talaxian= Toolaxian
Tanis= Tarnish
Tellerium= Foolerium
T'Pel= T'Fal
Troi= Ploy
Tuvok= Tictoc
Voyager= Toyager
Vulcan= Shmulkin
Warp= Whoomp
Worf= Woof
Wormhole= Porthole
Zimmerman= Swimmerman

Episodes (in order of airdate)
season one

Caretaker= Who gives a Care
Parallax= Paralaxitive
Time and Again= Not Time Again!
Phage= Pizzaface
The Cloud= Clouding the Issue
Eye of the Needle= Pin This!
Ex Post Facto= Ex Lax Facto
Emanations= Emmy-Nations
Prime Factors= Fractions and Primer
State of Flux= State of Flicks
Heroes and Demons= Doctor Who vs. Grendel
Cathexis= Casual-sex-us
Faces= About Faces
Jetrel= Intel
Learning Curve= Grading Curve

season two

The 37's= The Thirty-somethings
Initiations= Infertilization
Projections= Unidentified Projected Guest Stars
Elogium= Elongation
Non Sequitur= Nonsense
Twisted= Pretzel
Parturition= Partial Tuition
Persistance of Vision= Drug Induced Visions
Tattoo= Chuckuptay's Butt Tattoo Revealed
Cold Fire= Hot Ice
Maneuvers= Maneur
Resistance= ?????
Prototype= Pro-toe-type

Threshold= Fleshold
Death Wish= Deadly Games

other series episodes
Encounter at Farpoint= Encounter at Nearpoint
Yesterday's Enterprise= Yesterday's Doorprize
The Naked Time= The Nudey Bar

words I think we still need parodies for:
um... surely there are others?...