Avoid using Many to Many Relationship I have a 3 tables, Employee, Languages, Employee Languages.

Now, Employee table is a profile table. Nothing special(Id, first name, last name etc.). 

Languages table has two columns: Language ID column and Language name column. This table, basically is a list of all languages.

Employee Languages consists of three columns: Employee ID, Language ID and Proficiency.

So, when I want to show employee languages, I have to get language id, then correlate that id to language name and then show it to the end user.

I'm currently thinking about new scenario with two tables:

First would be Employee table.

Second would be Employee Languages, which consists of Employee ID, Language Name and Proficiency.

So, Language name and Proficiency would be populated in front end and would be shown as a drop down list. 

My question is which scenario would be much more effective in my case?
Your 2 table design approach can be implemented using a view. This would not compromise your underlying database design based on 3 tables. 

Views are under used but often give the best of all worlds.

Expanded:

From your "normalised" 3 table design, which looks OK, you will CREATE VIEW (SELECT Employee ID, Language Name, Proficiency FROM Employee, Languages, Employee_Languages WHERE etc. ). Your application then selects from the view.