If you help out pirate ships, or other aliens, do they remember so that your next encounters with them are more friendly?

As far as I can tell, no. That said, there is at least one encounter that can have, ah, repercussions depending on how you act.

Thanks! Not sure I've encountered that encounter with later repercussions or not yet. Unless you mean the stasis pod which I followed through to the end.

Actually, the repercussions are somewhat more immediate, but they can be unpleasant. Without giving too much away, if you refuse to help someone, if they survive without your help, they will get royally pissed and tell the rebel fleet where you are.

Ah that. Well almost all events have immediate repercussions of one kind or another. I've lost count of the crew members I've lost to giant spiders, infections, etc etc...

I don't think there's any such tracking. I'll take pirate bribes or ignore requests for help, but the good guys still gladly help me out later. Maybe I'm travelling so fast, word just hasn't got to them yet. :P