Gone are those days when a job seeker used to look for a job in the newspaper and apply for it via postal mail. In this Digital Age, everything is done via E-mail. A job seeker signs up to many job listing sites and applies for a job from there. But, in many instances your mail, your profile doesnt reach the concerned person. Maybe the formatting is wrong, maybe your mail reaches the spam folder etc. So to avoid these things the best way to apply for a job to do some research about the company.
For example, you got a mail about an opening at Wipro on Naukri. So that job would be listed on their website on their career section. Upon reaching there apply directly. Your chances increases as the template there is different than Naukri. You can mention your preferred skills, what are you looking for etc.
Other than applying via career, you could do a bit more research and find information about the hiring person. Like his/her email, work number etc. A simple google search will give you this information. By reaching concerned persons work mail and sending resume directly boosts your chance of being shortlisted.