It depends in which Pokemon game, but in the newest games (Diamond/Pearl) You will need to earn badges to get a higher level for them to obey. if you have all 8, all Pokemon will obey you.
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It would be either that the Pokemon are too high of a level for your current badge command or tha you obtained them from trades.
These are the Gym Badges that make your Pokemon obey:Knuckle Badge: Pokemon up to level 30 obey you.Heat Badge: Pokemon up to level 50 obey you.Feather Badge: Pokemon up to level 70 obey you.Rain Badge: All Pokemon regardless of their level will obey you.
Pokemon Gold Trades Are not possible, However, the Updated "Heart Gold" and "Soul Silver" versions have trades. these trades can be commenced in any Pokemon center. On the top floor, in the "Union Room."
Badges allow Pokemon obey to a certain level. Once you get all badges, any traded Pokemon will obey at any level.
Once you beat a gym leader you can get a certain level of pokemon to obey you.