The great piece of software that makes exactly this possible is called Scrivener. Unfortunately though, it is only available on Mac and now a beta-version for Windows PC. I still mention it in case anyone on any of those platforms interested in the question ends up here, as the title doesn't mention the Linux-specificity. I wrote more about Scrivener in my answer to this question: Is there a special software for writers?
A piece of software I heard is very similar in features, and is supported on the Linux platform as well, is Writer's Cafe. I cannot compare them myself, as I lack any experience with the latter, but it should be worth testing out.
Even though I cannot directly help with Linux software, I will elaborate on analog options. These will always be less streamlined than using dedicated software, as the organization has to be done manually.
The best way would be to have folders with printed out/jotted down text, organized by project. So, if you have a scene that you want to use in a certain project, only later on, get it on a piece of paper and file it in the folder. You then always know where to look. It is also a good idea to color-mark, or otherwise mark the papers for sub-sorting, and you can clip small cards with a synopses in the top corner for even more clarity. Again, the exact system is up to you, and will have to be manually maintained.
Generally I would recommend to have one folder per working project, plus a 'Misc' folder for all those great ideas that you have had which aren't strictly part of an already existing project (maybe they will become seeds of future projects).
I hope this helps a little and good luck organizing and sorting.
P.S. You can of course use boxes instead of folders, or anything else that suits you personally.