These security and cryptography papers are among the most cited between the years 2013 and 2014. Source data is from Google Scholar Metrics. The papers are roughly in the order of citations per year. More recent 2015 and 2016 publications haven't accumulated enough citations to make the list yet.

1. Candidate Indistinguishability Obfuscation and Functional Encryption for all Circuits
   S Garg, C Gentry, S Halevi, M Raykova, A Sahai, B Waters
   FOCS, 2013
   
2. Candidate Multilinear Maps from Ideal Lattices.
   S Garg, C Gentry, S Halevi
   Eurocrypt, 2013
   
3. FRESCO: Modular Composable Security Services for Software-Defined Networks.
   S Shin, PA Porras, V Yegneswaran, MW Fong, G Gu, M Tyson
   NDSS, 2013
   
4. Homomorphic Encryption from Learning with Errors: Conceptually-Simpler, Asymptotically-Faster, Attribute-Based.
   C Gentry, A Sahai, B Waters
   Crypto, 2013
   
5. Path ORAM: an extremely simple oblivious RAM protocol
   E Stefanov, M van Dijk, E Shi, C Fletcher, L Ren, X Yu, S Devadas
   ACM CCS, 2013
   
6. Practical Multilinear Maps over the Integers.
   JS Coron, T Lepoint, M Tibouchi
   Crypto, 2013
   
7. Message-Locked Encryption and Secure Deduplication.
   M Bellare, S Keelveedhi, T Ristenpart
   Eurocrypto, 2013
   
8. How to use indistinguishability obfuscation: deniable encryption, and more
   A Sahai, B Waters
   STOC, 2014
   
9. Pinocchio: Nearly Practical Verifiable Computation
   B Parno, J Howell, C Gentry, M Raykova
   IEEE S&P, 2013
   
10. Zerocoin: Anonymous Distributed E-Cash from Bitcoin
    I Miers, C Garman, M Green, AD Rubin
    IEEE S&P, 2013
    
11. DREBIN: Effective and Explainable Detection of Android Malware in Your Pocket.
    D Arp, M Spreitzenbarth, M Hubner, H Gascon, K Rieck
    NDSS, 2014
    
12. DupLESS: Server-Aided Encryption for Deduplicated Storage.
    S Keelveedhi, M Bellare, T Ristenpart
    USENIX Security, 2013
    
13. ZMap: Fast Internet-wide Scanning and Its Security Applications.
    Z Durumeric, E Wustrow, JA Halderman
    USENIX Security, 2013
    
14. A Heuristic Quasi-Polynomial Algorithm for Discrete Logarithm in Finite Fields of Small Characteristic.
    R Barbulescu, P Gaudry, A Joux, E Thomé
    Eurocrypt, 2014
    
15. Attribute-Based Encryption for Circuits from Multilinear Maps.
    S Garg, C Gentry, S Halevi, A Sahai, B Waters
    Crypto, 2013
    
16. Reusable garbled circuits and succinct functional encryption
    S Goldwasser, Y Kalai, RA Popa, V Vaikuntanathan, N Zeldovich
    STOC, 2013
    
17. Practical Control Flow Integrity and Randomization for Binary Executables
    C Zhang, T Wei, Z Chen, L Duan, L Szekeres, S McCamant, D Song
    IEEE S&P, 2013
    
18. Attribute-based encryption for circuits
    S Gorbunov, V Vaikuntanathan, H Wee
    STOC, 2013
    
19. Just-In-Time Code Reuse: On the Effectiveness of Fine-Grained Address Space Layout Randomization
    KZ Snow, F Monrose, L Davi, A Dmitrienko, C Liebchen, AR Sadeghi
    IEEE S&P, 2013
    
20. Lucky Thirteen: Breaking the TLS and DTLS Record Protocols
    NJ Al Fardan, KG Paterson
    IEEE S&P, 2013
    
21. Virtual Black-Box Obfuscation for All Circuits via Generic Graded Encoding.
    Z Brakerski, GN Rothblum
    TCC, 2014
    
22. AppIntent: analyzing sensitive data transmission in android for privacy leakage detection
    Z Yang, M Yang, Y Zhang, G Gu, P Ning, XS Wang
    ACM CCS, 2013
    
23. FLUSH+ RELOAD: A High Resolution, Low Noise, L3 Cache Side-Channel Attack
    Y Yarom, K Falkner
    USENIX Security, 2014
    
24. RSA Key Extraction via Low-Bandwidth Acoustic Cryptanalysis.
    D Genkin, A Shamir, E Tromer
    Crypto, 2014
    
25. Vetting undesirable behaviors in android apps with permission use analysis
    Y Zhang, M Yang, B Xu, Z Yang, G Gu, P Ning, XS Wang, B Zang
    ACM CCS, 2013
    
26. Zerocash: Decentralized Anonymous Payments from Bitcoin
    EB Sasson, A Chiesa, C Garman, M Green, I Miers, E Tromer, M Virza
    IEEE S&P, 2014