Company not providing form 16, is it legal?
If the company has not deducted any taxes, they are not legally bound to issue form 16. As a general practise most companies issue it.
If a company has deducted taxes, it is legally mandetory for the company to provide form 16 and is covered under Rule 31, section 203 of income tax act. The due date is after the end of financial year.
How can I file taxes?
If you have all the salary slips that give the details of salary paid and taxes deducted, you can still file the returns. You would also need TAN of the company, if you don't have this from previous form 16, you can get this from Form 26AS. This Govt website actually shows how tax was deducted by the company and deposited with the government against your PAN card.
What if he gives salary certificate without exempting all the allowances (according to section 10) I will be in a condition to pay more tax.
Generally Salary Certificate is of not much use, it will only give the gross amount without any break-up. The best course of action is registering yourself so that you can see Form 26AS and calculating taxes from there. Further you can formally write to your company pointing out relevant Income Tax rules. If they still don't agree, you can file a grievance with Income tax department.