MySQL case statement with two tables
You can simplify if(col is null,0,col) as ifnull(col, 0).

The SQL keywords are inconsistently formatted.
Sometimes you write SELECT, other times as Select.
I suggest to stick to all caps always.
The same goes for if (and ifnull) and as too.
It's easier to read the code when the writing is consistent.

The last line of your script is very long,
and it's difficult to read when I have to scroll to the right and the left part goes out of sight.
I suggest to add a few line breaks in there to make the code fit within one horizontal window. (I see you updated your original post, now it's good.)

It would be better to indent the sub-query more, and to put the closing ) on a new line to make it more visible. Something like this:

SELECT IFNULL(roll, 0) AS roll, 
       IFNULL(cpapername, 0) AS compulsory,
       IFNULL(corepapername, 0) AS Core, 
       IFNULL(e1papername, 0) AS Elective1,
       IFNULL(e2papername, 0) AS Elective2
       FROM (
           SELECT student.univ_roll AS roll, student.name AS name, student.rollno AS rollno, 
           (CASE WHEN student.compulsory = paper.subject
             THEN (paper.paper_name) END) AS cpapername,
           (CASE WHEN student.core= paper.subject
             THEN (paper.paper_name) END) AS corepapername,
           (CASE WHEN student.elective_I= paper.subject
             THEN (paper.paper_name) END) AS e1papername,
           (CASE WHEN student.elective_II= paper.subject
             THEN (paper.paper_name) END) AS e2papername
            FROM student, paper WHERE student.semester='First' 
            AND student.batch='2014' AND student.class='BSc' 
            AND student.semester=paper.semester AND student.batch=paper.batch 
            AND student.class=paper.class  AND student.regd='1'
    ) r