Question: Let's say I play a necromancer and have raised some Skeletons or Zombies using Animate Dead and some Gouls, Ghasts, Wights or Mummies using Create Undead.

When I use a bonus action to command them can I command all the undead I have with single bonus action even though they were created with different spells?

Answer: 
No, you can only command the creatures created by one of the spells when you use your bonus action.
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While both spells state that they require a bonus action, both of them only allow you to command creatures you made with that particular spell.

Here is the relevant rules text for *Animate Dead*:

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> On each of your turns, you can use a Bonus Action to mentally Command **any creature you made with this spell** [...]
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As well as the rules text for *Create Undead*:

> 
> As a Bonus Action on each of your turns, you can mentally Command **any creature you animated with this spell** [...]
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No
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The spells lists the option as follows (**emphasis** mine)

> 
> On each of your turns, you can use a bonus action to mentally command any creature you made with **this spell** 
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Since you can only command creatures created by the specific spell, any other creatures are not commanded, even though the spells are related.