2 Removed incorrect licensing comment.
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If you put three instances on the VM, you will have 3 copies of SQL Server running, using 3 licenses.  

If you put the 3 databases into a single instance, then you have only 1 copy of SQL Server running on your VM which makes more memory, processor, etc available to your processes.

Assuming no serious processing issues, I would recommend the single instance. Why add overhead unless there is some other compelling reason to do so?

If you put three instances on the VM, you will have 3 copies of SQL Server running, using 3 licenses.  

If you put the 3 databases into a single instance, then you have only 1 copy of SQL Server running on your VM which makes more memory, processor, etc available to your processes.

Assuming no serious processing issues, I would recommend the single instance. Why add overhead unless there is some other compelling reason to do so?

If you put three instances on the VM, you will have 3 copies of SQL Server running.

If you put the 3 databases into a single instance, then you have only 1 copy of SQL Server running on your VM which makes more memory, processor, etc available to your processes.

Assuming no serious processing issues, I would recommend the single instance. Why add overhead unless there is some other compelling reason to do so?

1
source | link

If you put three instances on the VM, you will have 3 copies of SQL Server running, using 3 licenses.

If you put the 3 databases into a single instance, then you have only 1 copy of SQL Server running on your VM which makes more memory, processor, etc available to your processes.

Assuming no serious processing issues, I would recommend the single instance. Why add overhead unless there is some other compelling reason to do so?