As of June 2023, there are three active branches of GnuPG: 2.4, 2.2, and 1.4. GnuPG versions 2.4.1 and later suffer from GnuPG bug T6481 and are hardly usable with Emacs. There is a patch for that bug available at least for GnuPG version 2.4.1, which your operating system or distribution might provide already. GnuPG 1.4 is considered a legacy version.
Besides that, all of those branches mentioned above should work flawlessly with Emacs with basic use-cases. They have, however, some incompatible characteristics, which might be visible when used from Emacs.
gpg-agent. The GPG_AGENT_INFO
environment variable, which is used by GnuPG 2.0 and 1.4, is ignored.
That means, if your system has both GnuPG 2.1 and 1.4, the gpg command
from GnuPG 1.4 is not able to use gpg-agent provided by 2.1
(at least out of box).