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Algebraic Number Theory Archive - Number theory/arithmetic geometry. (~200 articles)
 
Banach Space Bulletin Board - Banach spaces/functional analysis. (~400 articles, arXiv overlay)
 
Conservation Laws Preprint Server - Analysis/simulation of conservative PDEs. (100+ articles)
 
Cryptology ePrint Archive - of the IACR
 
European Singularities Network - Singularities in geometry and complex analysis. Searchable index (100+ articles).
 
Evolve-L archive - Evolution equations and semigroups. (100- articles)
 
Field Arithmetic Archive - This archive stores electronic preprints on the arithmetic of fields, Galois theory, model theory of fields, and related topics.
 
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 - and related structures (~50 items)
 
MGNet Preprints - Multigrid and other methods for PDE simulation. (100+ articles)
 
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)
 
Online Theses in Number Theory - ~35 items.
 
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.
 
SCAD: Preprints on Systems and Control - Links to archives which contain preprints in the general area of systems and control theory.
 
Shelah's Archive - Papers by Saharon Shelah in logic and related. (100s of articles, arXiv mirrored)
 
 
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