Certificating in general

Marc Branchaud's MSc thesis, the best starting point
List of PKI links
CIT PKI Group (look at their General Help for a good linklist)
PKI project Oscar
NIST PKI programme
PKI Standardization Homepage
Swedish project SEIS, see also EID Certificate specification
SEIS mailing list archive
Baltimore Technologies, see also their partners for a good list of PKI companies
Public Key Infrastructure Study: Final Report by Shimshon Berkovits, Santosh Chokhani, Judith A. Furlong, Jisoo A. Geiter, and Jonathan C. Guild (original link is here)
The PKI page - a lots of PKI-related links

Some companies and their papers

VeriSign
VeriSign reopsitory
VeriSign Certification Practice Statement, introduction
Netscape Certificate Extensions (can be a bit out of date)
CAs providing services for MS products
ECOM (Japan)
IAIK Java Security, see also their specification
OnWatch.com (public-key.com)
www.usertrust.com/
AlphaTrust
E-Trust
Baltimore and its whitepapers.

Digaital Signatures

Digaital Signature Links by Juan Avellan
Digital Signature Law Survey by Simone van der Hof

Notary - working groups and companies

CyberNotary Committee Home Page at ABANet.org
Digital Notary Service by Surety
Entropia Internet Notary Service (or further:https://entropia.com/notary/)
Digital Notary Service in Korea
Towards the Formulation of Guidelines for Digital Notary Systems by ECOM (some kinds of their related progress reports can also be found here and here and here and here)
Firstuse.com
E-Timestamp.com
NetDox.com
IDMetrix.con
Russian program Notary
Entegrity.com's Notary 2.0

Articles

Establishing Identity Without Certification Authorities by Carl M. Ellison
Transient-key digital time-stamps, a kind of general talk

X.509

ICE-TEL Certification Infrastructure
German Policy Certification Authority
Jozef Stefan Institute Digital ID Center (ICE-TEL)
Visa SET
SET Documentation by SETCo
SET Message Definition
What does Netscape do with the certificates?

PKIX - PKI using X.509; IETF stuff

PKIX Working Group
PKIX mailing list
PKI related Internet drafts
Certificate and CRL Profile - An Internet draft (check for more in the same directory)
Time Stamp Protocols - An Internet draft
Data Certification Server Protocols - An Internet draft
Notary Protocols - An Internet draft

Certificate revocation

My own overview of Certificate Recocation Paradigms
ValiCert's Certificate Revocation Trees.
Certificate Revocation: Mechanics and Meaning by Barbara L. Fox and Brian A. LaMacchia
Efficient Certificate Revocation by Silvio Micali
Certificate Revocation Modeling by NIST; see the paper by David Cooper
Can We Eliminate Revocation Lists? by Ron Rivest
Certificate Revocation and Certificate Update by Moni Naor and Kobbi Nissim
X.509 Internet Public Key Infrastructure: Online Certificate Status Protocol - OCSP, Internet Draft
X.509 Internet Public Key Infrastructure: Caching the Online Certificate Status Protocol, Internet Draft
ENHANCED CRL DISTRIBUTION OPTIONS - An Internet draft

PKCS - an RSA standard

What is PKCS?
Download PKCSs 1-10 plus some extras
Netscape's PKCS11
Netscape's PKCS11 FAQ
PKCS11 by RSA Labs
PKCS12 by RSA Labs (draft)
PKCS13 by RSA Labs (elliptic curve cryptography standard, draft)
PKCS15 by RSA Labs (smart card file format, draft)
PKCS draft

Other paradigms

SDSI/SPKI

Generalized Certificates (ideology behind SPKI)
SDSI

DNS Security Extensions

An Internet draft (check for more in the same directory)

PGP Certificates

pgp.net
Robert (Guerra)'s PGP links
International PGP

Meta-Certificate Group

http://www.mcg.org.br
USA mirror
Meta Certificate Premier
Certification: Extrinsic, Intrinsic and Combined
Overview of Certification Systems: X.509, CA, PGP and SKIP

Miscellanea

S/MIME Working Group
Stefan Kelm's PKI link list
Microsoft Wallet
OID Registry
A strange document. (Seems to be out of date.)
INFOSEC - one more European thing
ftp://ftp.bull.com/pub/OSIdirectory (see particularily ITU/ and Phoenix98Output/ directories)
Package java.security.cert
Microsoft security (Netscape, beware!)

Abbreviations

Hunting throughout this materials I found several confusing abbreviations, so I wrote them down here together with some clarifications.