I'll answer all of them so far to the best of my ability
1. Which boss does Samus fight first in Metroid: Zero Mission?
no idea
2. What wise amphibian guides you in Super Mario RPG?
Frogfucious
3. How many dog breeds are there in the Nintendogs universe?
maybe 30?
4. What was the first game to star Luigi?
do you mean just luigi, or luigi's first appearance? if the former, Luigi's Mansion. Other wise, Mario Bros.
5. What Pokemon is featured on the Pokemon Pearl game box?
no idea
6. In Mario Bros., how many hits will make the POW disappear?
Three
7. How many different forms of the Pokemon Deoxys are there?
two
8. In Super Mario Bros. 3, who is the boss of the fortress?
...some koopa guy, I forgot :/
9. In Super Mario Bros. 3, what could Tanooki Mario transform into?
Statue
10. In Donkey Kong, what weapon does Mario use to counterattack?
Hammers
11. What was Mario's profession in the 1981 Donkey Kong arcade game?
Construction worker
12. In what year was Mario Bros. released?
1984
13. In what year was the Donkey Kong Jr. arcade game released?
1983
14. Who runs the boat house in Noki Bay in Super Mario Sunshine?
no idea
15. What is the name of the Star Fox battle cruiser?
Arwings
16. The Star Fox team pilots what fighters?
Andross
17. What wingman betrayed James McCloud?
Either it was Peppy Hare, or Peppy's dad. I'm not firing up Starfox 64 right now either.
18. Punch Out! Featuring Mr. Dream features Mario in what role?
Referee
19. In which game did Mario wear a sombrero?
no idea
20. True or False: In Luigi's Mansion, Mario is trapped inside a painting?
I believe that's true