I think I realize now that org-mode + TeX is the best combo.
Writing in org is second nature at this point, but also being able to export as a pdf using a TeX template is pretty insane to me.
I think everyday I learn something new about org that makes me wonder why I used other tools.
They are also good long-term solutions IMO.
Plain TeX seems to be pretty portable by all accounts, and there are enough people supporting it. Efforts like KerTeX look very promising.
Emacs has made it this far, so I don't see any reason why it won't keep thriving. Org has the advantage of being plain text, so even if emacs and org-mode explode, the format itself could live on.
Merveilles is a community project aimed at the establishment of new ways of speaking, seeing and organizing information — A culture that seeks augmentation through the arts of engineering and design. A warm welcome to any like-minded people who feel these ideals resonate with them.