Approach 1, works if the size of the matrix is $\geq 6$.
Step 1. Generate a diagonal matrix $\geq 6$ with all eigenvalues distinct.
Step 2. Pick 500 distinct permutations on the rows of that matrix. (There are a total 6! = 720 permutations, so you are guaranteed to have 500 distinct ones.)
If the size of the matrix is smaller (say, 4), repeat steps 1-2 above for two or more different sets of 4 distinct eigenvalues.
Approach 2 (less cheap, but more versatile and also generates more interesting matrices):
Do two similar matrices count as distinct? [https://en.wikipedia.org/wiki/Matrix_similarity] If so, you can proceed as follows:
- Generate a diagonal matrix $D$ with the desired (integer) eigenvalues.
- Generate an invertible matrix $A$ of the same size as $D$.
- Record the matrix $A^{-1} D A$.
Repeat steps 1-3 or (if you want to keep the same eigenvalues) just the steps 2-3, making sure no two $A$'s repeat.