Aliens all look like overly sun-tanned humans with black polar neck sweaters and "Zorro" mustaches (ST:OS).
Aliens all look like humans with cut up bits of old vinyl sofas glued to their foreheads (ST:TNG).
Everybody speaks English.
All alien planets always only ever look like one particular earth location in every episode of a given series (the Arizona desert in "Star Trek", Welsh slate quarries in "Blake's Seven", coniferous forests in "SG1", cheap-looking soundstage sets in "Space 1999" etc.).
Technology keeps breaking down (either of its own accord, or due to this week's "mystery special guest radiation" a la ST:TNG), jeopardising the crew.
There always has to be somebody completely stupid who knows nothing around so that someone else can explain plot elements and tech to them (see Deanna Troi, ST:TNG).
Thou shalt have at least one "evil twin" episode per season.
Thou shalt have at least one "alternate reality" episode per season.
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"Heeeeeeeeeeeeere's Johnny!"