Torus-based cryptography
XTR http://en.wikipedia.org/wiki/XTR
CEILIDH has separate page, but can do more torus-based crypto, too.

Hyperelliptic curves
http://en.wikipedia.org/wiki/Hyperelliptic_curve
quite a bit of stuff in http://en.wikipedia.org/wiki/Imaginary_hyperelliptic_curve

Hyperelliptic curve primality proving

Number theoretic pseudorandom number generators
Pages
http://en.wikipedia.org/wiki/Pseudorandom_number_generator  
http://en.wikipedia.org/wiki/List_of_pseudorandom_number_generators
do not cover the number theoretic constructions; only ones mentioned are
http://en.wikipedia.org/wiki/Linear_congruential_generator
http://en.wikipedia.org/wiki/Inversive_congruential_generator
but power generator, Naor-Reingold, and elliptic curve versions coul be added


Message authentication codes based on number theory
http://en.wikipedia.org/wiki/Message_authentication_code
VMAC, Badger, MMH, Gilbert-McWilliams-Sloane 


Factorization:
H.W. Lenstra & C. Pomerance :A rigorous time bound for factoring 
integers and related algorithms (Schnorr, Seysen)
Joux et al paper at Asiacrypt'09


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Lots of Dutch pages:

All of the above + NTRU, point counting on elliptic curves, 
exponentiation, secret sharing


Planetmath