How do I collect all the goons?

In addition to what badp said here, you can follow a very similar strategy, without the need to hit repair.

If your current goons exceeds your "Desired Surplus Crew" (indicated by a little + icon next to your ships current crew levels) you can press U to jetison all of your excess crew. If you do so near your beacon, the beacon will automatically begin to suck up all the ejected goons.

This method can be much faster if you're already near your beacon, as it eliminates all of the time spent warping out, repairing and warping back in. The only time you lose is any travel time to and from the beacon.

So long as:

• your mothership has room for additional goons, and
• the beacon to the current area is active

You can simply order your ships to repair from the Tactics pane (F2 or Spacebar). This will make them immediately go back to the mothership for, well, repairing; in addition they will also drop excess goons (and rez).

You determine how many goons are excess goons with the "Desired Surplus Crew" slider in the Hangars pane (F3).

If the beacon has been destroyed, your only option to leave the sector is a mass retreat; as a result you'll have to leave all escape pods to their gloom destiny. If there's no beacon because you're at your mothership hideout, you can still order your ships to repair but it'll take longer as the ships need to physically travel the distance to and from the mothership back and forth in the process. To avoid this you can refit your ship by changing its loadout slightly from the Hangars panel.