The RSA cryptosystem introduced in 1977 by Ron Rivest, Adi Shamir and Len Adleman is the most commonly deployed public-key cryptosystem. Elliptic curve cryptography (ECC) introduced in the mid 80's by Neal Koblitz and Victor Miller is becoming an increasingly popular alternative to RSA offering competitive performance due the use of smaller key sizes. Most recently hyperelliptic curve cryptography (HECC) has been demonstrated to have comparable and in some cases better performance than ECC. The security of RSA relies on the integer factorization problem whereas the security of (H)ECC is based on the (hyper)elliptic curve discrete logarithm problem ((H)ECDLP). In this thesis the practical performance of the best methods to solve these problems is analyzed and a method to generate secure ephemeral ECC parameters is presented. The best publicly known algorithm to solve the integer factorization problem is the number field sieve (NFS). Its most time consuming step is the relation collection step. We investigate the use of graphics processing units (GPUs) as accelerators for this step. In this context, methods to efficiently implement modular arithmetic and several factoring algorithms on GPUs are presented and their performance is analyzed in practice. In conclusion, it is shown that integrating state-of-the-art NFS software packages with our GPU software can lead to a speed-up of 50%. In the case of elliptic and hyperelliptic curves for cryptographic use, the best published method to solve the (H)ECDLP is the Pollard rho algorithm. This method can be made faster using classes of equivalence induced by curve automorphisms like the negation map. We present a practical analysis of their use to speed up Pollard rho for elliptic curves and genus 2 hyperelliptic curves defined over prime fields. As a case study, 4 curves at the 128-bit theoretical security level are analyzed in our software framework for Pollard rho to estimate their practical security level. In addition, we present a novel many-core architecture to solve the ECDLP using the Pollard rho algorithm with the negation map on FPGAs. This architecture is used to estimate the cost of solving the Certicom ECCp-131 challenge with a cluster of FPGAs. Our design achieves a speed-up factor of about 4 compared to the state-of-the-art. Finally, we present an efficient method to generate unique, secure and unpredictable ephemeral ECC parameters to be shared by a pair of authenticated users for a single communication. It provides an alternative to the customary use of fixed ECC parameters obtained from publicly available standards designed by untrusted third parties. The effectiveness of our method is demonstrated with a portable implementation for regular PCs and Android smartphones. On a Samsung Galaxy S4 smartphone our implementation generates unique 128-bit secure ECC parameters in 50 milliseconds on average.