Onions
Red Onion

Houses red pikmin.
Yellow Onion

Houses yellow pikmin.
Blue Onion

Houses blue pikmin.
Other Ships
S.S.Dolphin

Olimers ship from pikmin 1 (complete version).
Research Ship

Olimer and Louie's research ship from pikmin 2, houses purple and white pikmin.
President Choochoo's Ship

It is solid gold. It houses purple and white pikmin. (No wonder they went in debt)