The courses that we take for GATE are like a complete story.

You can read topics

from different books as long as the story in your mind about the subject does n
ot miss a few characters. But there is a certain drawback. Who prepares the GATE
question papers? It is the IIT professors and they have their own set of books
that they are comfortable with. The questions and notations that would be used i
n the GATE exam are more likely to be from these books.
About how GATE is different from JEE: In JEE, you need to be a hard nut to crack
the exam. You need to know how to solve a particular type of question (that is,
if you are not intuitive enough to find the solution on your own, and that is w
hat is taught at all the coaching centres). In GATE, you need to have an in-dept
h knowledge about your specific field. The syllabus is vast and you cannot help
but study.
Here are some books that I used while preparing for GATE 2012.
Algorithms: Introduction to Algorithms by Rivest, Cormen, Stein, Leiserson,
generally known as clrs. There is no beating this book. It is like the bible fo
r a CS engineer.
Operating System: "Operating System Principles" by Galvin. I liked the book.
Read semaphores well and solve a lot of problems. There are a couple of other b
ooks by Tanenbaum and Stallings which could be useful for certain topics.
Theory of Computation: "Theory of Computation" by Ullman. The book is very h
ard on your eyes with so many weird symbols involved, but if you concentrate wel
l, you would get every point of it. Another one is "Introduction to the Theory o
f Computation" by Michael Sipser. This I fiound more helpful for interviews.
Computer Networks: "Computer Networking: A top-down approach" by Kurose-Ross
and "Computer Networks" by Tanenbaum, There have been questions in the past dir
ectly from Tanenbaum. But Kurose-Ross is what I preferred. There are other books
by William Stallings and Behrouz Forouzan which could be useful for certain top
ics. Forouzan is relatively easy but i don't advice you to read as the main book
for preparation.
Computer Organisation: "Computer Organisation" by Carl Hamacher. The problem
with this subject is that professors in IITs prefer Patterson, but the syllabus
for GATE is more in accordance with Hamacher.
Programming and Data Structures: Have a good hold on basic programming in C.
Coremen is good enough for data structures.
Graph Theory: "Graph Theory with Applications to Engineering and Computer Sc
ience" by Narsingh Deo. I personally did not refer to it for GATE exams but read
it for semesters. It is a good experience.
Database Systems: "Database System Concepts" by Korth
Compiler Design: "Principles of Compiler Design" by Aho and Ullman. Read par
sing well and also Syntax Directed Translation(SDT) well. .
Digital Logic: "Digital Logic and Design" by Morris Mano.
Software Engineering: "Software Engineering: A Practitioner's Approach" by P
ressman. Need not read the whole book but a few important concepts like Cyclomat
ic Complexity, Coupling and Cohesion, etc.
Web Technologies: Have an idea about basic HTML, XML, etc.