Algebraic Number Theory Archive: Number theory/arithmetic geometry. (~200 articles)
Banach Space Bulletin Board: Banach spaces/functional analysis. (~400 articles, arXiv overlay)
Center for Commutative Algebra: Preprint announcements and links.
Conservation Laws Preprint Server: Analysis/simulation of conservative PDEs. (100+ articles)
Cryptology ePrint Archive: At the IACR.
Groups, Representations, and Cohomology Preprint Archive: Algebraic topology/finite group theory. (100s of articles.)
Hopf Topology Archive: Algebraic topology and related areas. (~400 articles)
Jordan Theory Preprint Archives: Jordan algebras and related topics (~100 articles).
K-theory Preprint Archive: K-theory (generalized cohomology theories). (~400 articles)
Linear Algebraic Groups and Related Structures: Including Azumaya Algebras, Algebras with Involutions, Brauer Groups, Quadratic and Hermitean Forms, Witt Rings, Lie and Jordan Algebras, Homogeneous Varieties. DVI, PS, PDF (~80 items).
Markov Chain Monte Carlo Preprint Service: A list of all registered papers on MCMC methodology currently submitted for publication. Based at the Statistical Laboratory of the University of Cambridge.
Mathematical Physics Archive: Also called mp_arc; at UT Austin. (2000- articles)
MGNet Preprints: Multigrid and other methods for PDE simulation. (100+ articles)
Optimization Online: A repository of eprints about optimisation and related topics.
Probability Abstract Service: Probability Abstract Letters are sent about once every two months. The subscription is free.
Shelah's Archive: Papers by Saharon Shelah in logic and related. (100s of articles, arXiv mirrored)
Topology Atlas Preprints: Mostly general topology. (400+ articles)