The best way to apply for a job is through a referral. This is why networking is considered important in the corporate. Companies pay employees good referral bonuses to refer good candidates. Not only does referral provide you a better chance of being hired, but also helps to connect directly with the HR, provided you are in good terms with the person who referred you.
The next would be LinkedIn, provides a great platform to apply and connect directly with a recruiter.
Another great way is to visit the careers section of the company site, sure this takes a little time and can be repetitive for different companies, but still is a better way than 3rd party recruiting.
The worst way I would say is to be approached by a hiring agent or an online portal. These are just a waste of time as they mostly use your resumes for all the wrong purposes. And if you even get called for an interview, you will see its a pool hiring with 100s of other candidates.
