About certifications:
LPIC: http://www.lpi.org/
RedHat: http://www.redhat.com/certification/rhce/
About the documentation:
I mostly use the web for information.
Which distribution do you want to use?
For a Fedora system, this might be a good start (I'm a Fedora user):
http://www.howtoforge.com/perfect-server-fedora-12-x86_64-ispconfig-2
If you want Windows clients to connect and use Linux servers, then consider learning SAMBA at least. SAMBA is used for e.g. file & printersharing.
For a webserver, consider Apache, MySQL & phpMyAdmin.
For a mailserver, I would suggest Sendmail or Postfix for SMTP, and Dovecot for IMAP & POP.
ProFTP is nice for FTP features.