Aside from your NCERT books for Physics, Chemistry and Biology, these are the best books:
Physics: S.L Arora. Concepts are explained clearly in simple language. It has a variety of problems which can help you to hone your skills in Physics. The ‘Short answer conceptual problems’ section really helps one to tackle the theoretical questions and questions involving reasoning.
Chemistry: Comprehensive Chemistry and Xam Idea. The former can be used for detailed study of the chapters along with JEE preparation. The latter can be used for quick revision and checking out the board questions of previous years.
Biology: Xam Idea. The ‘Basic concepts’ section of this book has extra stuff which can help you to answer questions which you don’t feel are based on NCERT. For example, the names of only 2 enzymes involved in DNA replication are given in the textbook, namely DNA Polymerase and DNA ligase. Xam Idea includes helicase and other enzymes which are also involved in DNA replication. As I mentioned above in the case of Chemistry, it contains the previous years’ board questions and is very useful.