There are 2 aspects the Salary the company pays you and the Cost to the company which is higher than Salary.
In older days the companies would tell you the salary and you would decide to join on that basis, however given the current competition quite a few companies tell you CTC , i.e. Cost to Company. This number looks higher and most try to join only to realize that it is not true. Hence if you are comparing salaries to 2 companies, you have to leave out quite a few items.
Company Contribution to PF
As per regulations, Employers are required to match the PF contributions by Employee to the extent of 12% of Basic. As a practise most organization deduct 12% of basic and deposit it with PPF Office. An equal amount contributed and deposited by Employee.
As per regulations an organization must pay Gratuity after 5 years of completion of service at the rate of 15 days [last Drawn] Basic Salary for every year of Service completed. So if you leave after 5 years, you get 2.5 of Basic salary, if you leave after 8 years you get 4 of you Basic Salary
Edit to Clarify the comment
If your salary is Rs 1000, you pay a PF of Rs 100. The company pays a PF of Rs 100. Net you get Rs 900. Now what your company is saying is your CTC is Rs 1100, your PF deduction is Rs 100 and Company's contribution is Rs 100. You net is still Rs 900.