Ministry of Labor can force companies to pay you your dues but still Companies can play with time to delay it as much as possible. You should keep in mind that you will lose the job immediately then and wont get NOC. So if you are going for good, then go Ministry of Labor, I am fully sure you will get your due entitlements as I have dealt with Ministry of Labor.

As far as penalties are concerned, no there are no criteria for penalties set so far. Only MOL put black point against the company when an employee complain to MOL. Company has to close that complain in order to get done other Admin works related to MOL else company wont be able to do any visa change etc. The black point remain against the company forever. Surprisingly, if an employee complain to MOL and even employee loses the case by putting nonsense complain against company, still MOL put black point against company and it remains forever......

Future security on delayed salary payment, am not seeing it in near future in Qatar. If Qatar implements WPS( Wages Protection System) as UAE has , then the problem can cured but for now, employees have to bear atrocities of the bad companies...