• Upgrading from version 1.1
  You need to modify your sc_startweaps. sc_startweaps was modified to include the gauntlet and the machinegun. Therefore you need to set sc_startweaps to 6 if you want clients to start with the default set of weapons. If you've already modified sc_startweaps, just add 6 to your current value to maintain the same effect.
  For new cvars between 1.1 and 1.2, check HERE.
  
• Upgrading from version 1.2
  There's nothing to worry about if you're upgrading from 1.2.  You may want to know, however, that there are a couple of new things that default to being on or defined.  sc_firstspawn_message defaults to having a message, and sc_kick_spectator_bots defaults to being turned on.
  For new cvars between 1.2 and 1.3, check HERE.
  
• Upgrading from version 1.3
  The only thing you have to worry about when upgrading from 1.3 to 1.4 is your set of spawnvars.  If you created a custom spawnvar file, it is incompatible (and will prevent the server from loading the map) with the new system in 1.4.  See the Spawnvar help section.
  If you have any spawnvars from previous installations (you most likely do) you need to remove them!
  For new cvars between 1.3 and 1.4, check HERE.
  
• Upgrading from version 1.4
  The "sc_firstspawn_message" has been removed in favor of the new ability to print the MOTD when the client joins the game.
  Since voting teamleader is now part of allowable voting, you'll need to update your sc_voteflags (add 4096) to maintain the same voting functionality you had before.
  "sc_scoreboard_hack" is on by default.  You shouldn't need to turn this off - but you deserve to know that it defaults to on.
  For new cvars between 1.4 and 1.5, check HERE.
  
• Upgrading from version 1.5
  The format for the scrotation file has changed.  You must remove all "set {}" statements.  See the files section for a new example scrotation.cfg file.
  IP's are no longer logged to the games logfile.  You must use the admin log to track people's IP addresses.
  Various cvars have been removed.  Please check the changelog for details.
  For new cvars between 1.5 and 1.6, check HERE.

Windows installer instructions (both SCTA and SCQ3A): 

All you need to do is download the installer and run it. By default, it will install everything - the code, server configs (asking if you want to overwrite your current configs or not), example configs, spawnvars, and the help files. If you choose not to overwrite your current configs, be sure to check out the new CVARs (see Upgrade Notes above).

Linux installation instructions (SCTA):

First-time installation

• Download the full SCTA tarball

• cd /path/to/quake3
• tar -xzf /path/to/downloaded-file.tar.gz

Upgrading

• Download the SCTA code
• cd /path/to/quake3/missionpack
• tar -xzf /path/to/downloaded-file.tar.gz
• Check out the new CVARs (see Upgrade Notes above) and update your configs accordingly

Linux installation instructions (SCQ3A):

First-time installation

• Download the full SCQ3A tarball
• cd /path/to/quake3
• tar -xzf /path/to/downloaded-file.tar.gz

Upgrading

• Download the SCQ3A code
• cd /path/to/quake3/scq3a
• tar -xzf /path/to/downloaded-file.tar.gz
• Check out the new CVARs (see Upgrade Notes above) and update your configs accordingly

Individual file locations:

SCTA:
qagamex86.dll -> /path/to/quake3/missionpack
qagamei386.so -> /path/to/quake3/missionpack
*.cfg -> /path/to/quake3/missionpack
helpfiles -> /path/to/quake3/missionpack/help
spawnvars (*.sv) -> /path/to/quake3/missionpack/spawnvars
scta.bat -> /path/to/quake3
go -> /path/to/quake3

SCQ3A:
qagamex86.dll -> /path/to/quake3/scq3a
qagamei386.so -> /path/to/quake3/scq3a
*.cfg -> /path/to/quake3/scq3a
helpfiles -> /path/to/quake3/scq3a/help
spawnvars (*.sv) -> /path/to/quake3/scq3a/spawnvars
scq3a.bat -> /path/to/quake3
go -> /path/to/quake3