Would TrueCrypt [0] be still fine for that task? (Its security audit did not reveal anything serious [1].) Is there a reason to use VeraCrypt (and trust some additional people)?
Is there anything more reliable than those two? I am especially interested in GNU/Linux.
[0] https://en.wikipedia.org/wiki/TrueCrypt
[1] Except privilege escalations, not relevant for QubesOS users.
Now, I prefer a solution which preserves the directory structure like EncFS and I make sure to backup.
Has been pretty reliable and widely available.