Just Purdue and Penn State have. Nebraska also took itself out of consideration two years ago (Miles first year).They have but not that often and it is basically frowned upon.
These schools have either taken themselves out years previously or declined an invitation.
Indiana (last year)
Illinois
Michigan - their coach just gave an interview that they will not be playing a post season tournament this year if it is not the NCAA / NIT
*There might be others, these are just the ones I know of for sure.