Before you start taking Linux certification courses, you need to have a clear idea why you need to have a Linux certificate. The answer to this question will narrow down the list of suitable courses to just a few and it will be easier to decide which Linux certification course is the best for you.
There are many top courses for Linux certification and it is not possible to tell which one is the best. Actually, for different people and different purposes the list of top courses for Linux certification varies. Consider whether you need a Linux certificate for a job or just to have an in-depth, systematic knowledge in Linux.
If you need a Linux certificate just to put your Linux knowledge in order, then any of the general Linux certifications, such as LPI or CompTIAs will do. If you need a Linux certification for a job, then this focuses your choice a bit. Most likely you will need a particular course – i.e. if you will be administering an Oracle database under Linux, you will benefit most if you take a certification course in Oracle under Linux rather than in Linux in general.
If you expect that a single Linux certification will make you a Linux guru or that it will kick start your career, this will hardly happen. Similar to any other IT certification, Linux certifications are just one more advantage of yours. Certificates are especially important if you don't have formal training (i.e. a university degree) but again, what matters most is what you can do and not how many tons of diplomas you have.