This is a pretty comprehensive list of all the cash awards and super weapons for the easy, medium, and hard levels on Star Fighter 3000. If any of these are incorrect, or anyone knows of any more, please email me.
 

I have used the cordinate system used by the game (letter, number), '½' means that it is half way between that letter/number and the next letter/number. Please note that these grid references are only approximate. I am also assuming that there are no super weapons or cash awards hidden in asteroids. If a level is not listed, then there aren't any bonuses on it as far as I know.
 

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Easy

 

Mission 1	Cash award (200) in turrets at (C, 4) and (C, 3½)
Mission 29	Super weapon in two factories around (F, 1)

 

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Medium

 

Mission 1	Super weapon in tree at (D½, 5½), cash award in bridge-like tower at (E, 1½)
Mission 6	Cash award (1000) in structure at (F, 5½)
Mission 9	Time limit. There is a cash award in every target
Mission 15	Cash award (500) in white office building at (F, 6), super weapon in bridge-like tower at (E, 2)
Mission 19	Cash award in hangar (H, 2½), cash award in little house thingy at (B½, 6½), cash award in statue at (B½, 6½), cash award in middle hangar at (C, 3), super weapon in tower at (F½, 5), cash award in structure at (G½, 3½), super weapon in gravestone at (E, 2)
Mission 26	Super weapon in missile turret at (B, 1), cash award (800) in tree at (F, 6), super weapon in tree at (H, 2)
Mission 27	The gravestone you want to complete the level is at (F½, 2), there's also a cash award in turret at (F, 7½), cash award in church at (E½, 7½)
Mission 29	Cash award (850) and two super weapons in the first building you blow up
Mission 30	Super weapon in tree at (D, 6), another super weapon in tree at (H, 4½)
Mission 31	Cash award in white office building at (D½, 4½), another cash award in white office building at (D½, 2)
Mission 32	Super weapon in type gravestone at (D½, 7½), super weapon in gravestone at (E, 5½),cash award in gravestone at (F, 7)

 

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Hard

 

Mission 6	Cash award (100) in hangar at (G½, 2½), cash award (100) in all of the little houses around (A/B, 2/3), cash award (500) in gravestone at (F, 7), cash award in church at (F, 6), super weapon in gravestone at (D½, 7)
Mission 11	Cash award (1000) in white office building (D½, 2), cash award (1000) in white office building (D½, 4½)
Mission 21	Cash award (500) in tree (B, 1), super weapon in middle hangar (B½, 3), super weapon in tower (F,4), tower (B, 5), super weapon in tree (C, 7)
Mission 25	Super weapon in tree (D, 5½), cash award (500) in bridge-type tower (D½, 1½)
Mission 26	Cash award (850) and two super weapons somewhere
Mission 29	Cash award (500) in gravestone (F, 7), super weapon in gravestone (D½, 7½), super weapon in gravestone (E, 5½)
Mission 30	Super weapon in turret (A½, 5), cash award in tree (B, 3½)
Mission 32	Super weapon in tower at (A, 2)
Mission 33	Super weapon in gravestone (D½, 7), cash award (500) in gravestone (F, 7), super weapon in gravestone (E, 5½)
Mission 34	Cash award (1000) in container thingy (B, 5), and in the Christmas tree type structure at (B, 6)