Here's my first attempt.
There are very few ways to fill a 2x2 square, and none of those can be extended to allow a 3x3 square to be filled completely. The only way to fill a 2x2 square that does not involve a double is to arrange 4 dominoes like a windmill. I have tried to do that as often as possible in this solution. It contains all non-doubles except for 0-3, so 20 dominoes and 16 empty squares.
--- --- --- ------- --- --- ---
| . | . | 1 | 1 4 | . | . | 0 |
-------| |------- -------| |
| 6 5 | 5 | . | 4 | 4 6 | 6 |
------- -------| |------- ---
| . | 5 | 5 0 | 0 | . | 6 | . |
---| |------- -------| |---
| . | 4 | . | 0 | 0 1 | 1 | . |
--- -------| |------- -------
| 4 | 4 2 | 2 | . | 1 | 1 2 |
| |------- -------| |-------
| 3 | . | 2 | 2 3 | 3 | . | 2 |
-------| |------- -------| |
| 3 6 | 6 | . | . | 3 5 | 5 |
------- --- --- --- ------- ---
I have little doubt this can be improved by using doubles.
Edit:
I have now used a computer to find a better solution. The search was not exhaustive, but I suspect this is optimal.
This uses 23 dominos. The unused ones are: 1-6, 2-5, 3-3, 3-0, 4-0.
------- ------- ------- ---
| 1 1 | 1 2 | 2 2 | 2 |
------- ------- -------| |
| 1 | . | 1 | . | 2 | . | 3 |
| |---| |---| |--- ---
| 3 | . | 4 | 4 | 4 | 4 3 |
--- --- ---| |--- -------
| 3 | . | 4 | 4 | 4 | . | 3 |
| |---| |---| |---| |
| 5 | 5 | 5 | . | 6 | 6 | 6 |
---| |-------|---| |---|
| 5 | 5 | 5 6 | 6 | 6 | 6 |
| |--- -------| |---| |
| 1 | . | 5 | . | 0 | . | 2 |
-------| |------- -------|
| 1 0 | 0 | 0 0 | 0 2 |
------- --- ------- -------
Edit 2:
I have now done an exhaustive computer search, and if my program is correct then this is an optimal solution.