The World of SEXPs

From FreeSpace Wiki

TIP: You can get a brief description of all SEXPs supported in recent FSSCP builds by using the "-output_sexps" command line parameter.

What is the difference between ai-waypoints and ai-waypoints-once

AI-Waypoints-Once does just what you'd expect. The ship follows the way points you've given it and then comes to a rest at the last one. With AI-Waypoints however upon reaching the last waypoint the ship turns and heads for the first waypoint and begins the cycle again. This makes it very useful for setting up patrol routes etc.

Can I disable Alpha 1's subsystems?

Yep. Simply sabotage the subsystem you're interested in. Fred2 will complain at you but it will work.

IMPORTANT: There is a risk that messing with the subsystems of ships in the player squadron will cause the game to crash. This is because subsystems like "communication[s]" and "engine[s]" can be spelled with or without the S, and if the player changes his fighter class, he might choose one with a different subsystem spelling. This has been taken into account for FSO but remains a problem in retail. To avoid this, make the mission a scramble mission, or restrict the loadout to ships that have the same subsystem spelling.

How do I make a ship jump out at a certain place (e.g. a jump node)?

http://homepage.ntlworld.com/karajorma/freespace/FAQ-Images/Fred-Tips/NodeCapship.jpg
This depends greatly on the ship. Capships (or any ship that the player can't make jump out) can be done fairly easily. This is one way. You have to place a waypoint in the middle of the jump node. You then make the ship leave when it reaches a suitable distance either from the ship editor or by changing the ai-goal as above

If you're trying to stop Alpha 1 or a ship that Alpha can order to jump out requires a little more work. First you need to prevent the ship(s) from being able to jump out. Then you need to make it so that the ship can only jump out within a certain distance of the node.

http://homepage.ntlworld.com/karajorma/freespace/FAQ-Images/Fred-Tips/NodeJumpOnly1.jpg
http://homepage.ntlworld.com/karajorma/freespace/FAQ-Images/Fred-Tips/NodeJumpOnly2.jpg
http://homepage.ntlworld.com/karajorma/freespace/FAQ-Images/Fred-Tips/NodeJumpOnly3.jpg
The 2nd event activates the jump engines when alpha reaches 500m from the centre of the node. The 3rd event deactivates the engine if alpha leaves the area around the node. you'll need a repeat count on the 2nd and 3rd events or alpha 1 might be stuck in the mission. You might need to alter the distances too since I haven't checked them.

I noticed you are using never-warp. Why not break-warp?

Never-warp prevents the ship from leaving until the allow-warp order is given. Break-warp merely breaks the jump engine. It can be fixed by the fix-warp SEXP but it can also be repaired if the player docks with a support ship.

What is the difference between Ship-Invulnerable and Ship-Guardian?

Ship-Invulnerable means that a ship can't be damaged by anything. No matter what happens the ship will remain at 100% (or whatever the damage was when it was at when the SEXP triggered). Ship-Guardian allows a ship to take damage until the ship reaches 1%. After that the ship becomes invulnerable. Careful use of both can fool the player and prevent him from realising that the ship is protected (A wing of ships at 100% at the end of a mission is a big sign that Ship-Invulnerable was used while a wing at 1% is just as obviously a sign of Ship-Guardian's use. )

How Do I make a message come from a ship that isn't actually present?

If you look at a mission in FRED you'll notice that all orders from command are actually coming from #command. The # symbol tells FS2 that it's not coming from a ship that is actually present. Simply make the message come from #Whatever.

How do I make a Red-alert only occur when the player jumps out?

Easy. Just use an event like this
http://homepage.ntlworld.com/karajorma/freespace/FAQ-Images/Fred-Tips/RedAlert.jpg