Hmm... I always thought that the Goombas were a 'branch' of Bowser's army, like the Koopas and various other baddies. The Shy Guys, on the other hand, appear to be mercenary soldiers. This discussion came up (kind of) in another string. Someone listed the different bosses the shy guys have worked for...
Wart- SMB2
Smithy & Booster- SMRPG
Kamek- YI
Bowser- SM64 (fly guy?)