I am no stranger to "team" play. I have been in a few Quake clans, although I have never been a part of a truly prepared team with set courses and positions. This type of team is dangerous. I normally play FFA (Free For All) in JK, but I do venture into a Team or CTF game from time to time. Here are some tips when playing in these types of games.
Remember that although you can't kill your teammate, you DO damage their armor when attacking them. With this in mind, if you encounter your ally fighting an enemy, don't fire heavy weapons (Rail or Concussion) at them. This may drain your friends armor and allow his opponent to get the kill. If you wish to aid your teammate, use your Lightsaber, Repeater, or another "non-splash damage" weapon.
You CAN Blind your teammate. Watch that targeting!
You can Pull your friends weapon (if he doesn't have Absorb on). This is a problem that you can use to your advantage. If you see that your teammate doesn't have a heavy weapon (that's the great thing about JK, you can see the different types of weapons), type "pull" (hit T to send a message) and allow him to Pull one of your weapons (especially if you have both the Rail and Concussion). This will "spread the wealth" and is similar to passing weapons/ammo in Quake CTF.
I have seen team members travel together. In the one instance I witnessed this strategy, it was very effective.
I have left out quite a few things, including weapon/power-up camping, CTF strategies, etc. I hope to get both strategy and link submissions. I know there are some good team strat sites out there for Quake and they would be a good addition to this page. Please click the "Contact" to the left if you have anything to add.