My first instinct is something like $\frac{6!}{3!}$, but this overcounts, and is the result if every cube is unique. However, if the cubes are not unique, then really its just which holes are filled, which would be $2^6$, except that only up to 3 holes can be filled. This seems to be the same as the number of all unique unordered lists of the numbers 1-6 of length 0-3, but I'm not quite sure.
To be clear: the cubes are not unique, but the holes are unique.
Edit: Each hole can only hold 1 or 0 cubes.