I do not know what the final settlements are in your organization. But in general, the position regarding terminal settlements is as below:
1. Gratuity: In case the employee leaving has completed 5 years of service or is otherwise eligible for gratuity, the same is payable within 30 days from the date of separation. In case of delay, the liability for payment of interest will apply.
2. PF: Employers have no control over PF matters. In case PF is in a Company trust, the trust is liable to transfer the same if an application for transfer is received. In case PF is recovered from the last salary, the same needs to be remitted within 15 days to the concerned.
3. Cash equivalent of the balance of Leave: Can be held back until settlement of dues. In fact, I agree with Pratima. Dues can be recovered from or the shortfall in the notice period can be adjusted from leaves due.
4. Regarding the shortfall in the notice period, some companies (including mine) have delegated powers to authorities competent to accept resignations, to waive off the shortfall in the notice period, purely as a goodwill gesture. However, it is entirely up to the authority to accept proposals from HR for the waiver of the shortfall in the notice period. I think it is used in cases where the ex-employee is gracefully submitting a resignation.
5. Cases of 'absconding' employees need to be treated on a different footing. Considering pending assignments, knowledge ware, or other knowledge tools held by him/her at the point of separation, such cases need to be treated as matters of indiscipline if required. In which case, concessions given as a matter of goodwill would not be available to them.
6. I also agree with Girish. Your old employees are your best ambassadors. So, bid them goodbye with grace. Quick and hassle-free settlements would always be mutually beneficial. Go the extra mile to facilitate his/her smooth exit.
7. Finally, have a checklist and your response to various modes of separation for the settlement of benefits. If you can draw a scheme and obtain the consent of critical opinion-makers in your hierarchy, you can bring many smiles to ex-employees.