Relevant papers can easily be found using search engines like Google Scholar, CiteSeer, etc. Here is a short list of recent papers. Please note that I haven’t read any of them.
MD5
Guang Hu, Jianhua Ma, Benxiong Huang
High Throughput Implementation of MD5 Algorithm on GPU
Proceedings of the 4th International Conference on Ubiquitous Information Technologies & Applications, 2009. ICUT '09. pp. 1-5
Changxin Li, Hongwei Wu, Shifeng Chen, Xiaochao Li, Donghui Guo
Efficient implementation for MD5-RC4 encryption using GPU with CUDA
3rd International Conference on Anti-counterfeiting, Security, and Identification in Communication, 2009. ASID 2009. pp. 167-170
DES
Giovanni Agosta, Alessandro Barenghi, Fabrizio De Santis, Gerardo Pelosi
Record Setting Software Implementation of DES Using CUDA
2010 Seventh International Conference on Information Technology, pp.748-755
RSA
Owen Harrison and John Waldron
Efficient Acceleration of Asymmetric Cryptography on Graphics Hardware
Progress in Cryptology – AFRICACRYPT 2009
Lecture Notes in Computer Science, 2009, Volume 5580/2009, 350-367
Robert Szerwinski and Tim Güneysu
Exploiting the Power of GPUs for Asymmetric Cryptography
Cryptographic Hardware and Embedded Systems – CHES 2008
Lecture Notes in Computer Science, 2008, Volume 5154/2008, 79-99
AES
Deguang Le, Jinyi Chang, Xingdou Gou, Ankang Zhang, Conglan Lu
Parallel AES algorithm for fast Data Encryption on GPU
2010 2nd International Conference on Computer Engineering and Technology (ICCET), pp. V6-1 - V6-6
Chonglei Mei, Hai Jiang, J. Jenness
CUDA-based AES parallelization with fine-tuned GPU memory utilization
2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW), pp. 1-7
A. Di Biagio, A. Barenghi, G. Agosta, G. Pelosi
Design of a parallel AES for graphics hardware using the CUDA framework
IEEE International Symposium on Parallel & Distributed Processing, 2009. IPDPS 2009, pp. 1-8
Owen Harrison, John Waldron
AES Encryption Implementation and Analysis on Commodity Graphics Processing Units
9th Workshop on Cryptographic Hardware and Embedded Systems (CHES 2007), pp. 209-226
S.A. Manavski
CUDA Compatible GPU as an Efficient Hardware Accelerator for AES Cryptography
IEEE International Conference on Signal Processing and Communications, 2007. ICSPC 2007, pp. 65-68