I have Syncthing installed via pacman (since flatpaks cannot keep a daemon running). For every game that I care about, I find its save file, move it to a sync dir, and symlink it back to where it is expected. My savegame sync folder has folders for the many varied places that games like to hide their saves - "gamedir", local, locallow, "my documents", dot_config, etc. The most fun part is finding out where the appropriate proton prefix is.

If I was starting over again, there's a decky loader plugin that looks promising.

Syncthing and/or Warpinator.

If you have cloud storage available, either by a company or self-hosted, you can look into Ludusavi and OpenCloudSaves, both open source and using the same savegame path database.

Ludusavi is more mature with more features.

OpenCloudSaves aims to target better usability with the Deck specifically.

I haven't done this for game saves but you could probably use syncthing for this.

There's a decky extension that will automatically backup game saves to various cloud storage types.

For Epic and GOG games I use Heroic Launcher and for games that support it, it does the trick. The feature isn't fully stable yet and I remember specifying a path to saves manually, but once I did so, it synchronizes fine

I moved a Jubilee save from my Windows desktop to the Steam Deck once.

Never again. It's a hassle. I ended up only playing it on the Steam Deck henceforth.

By exclusively playing on Steam Deck there is no need to sync anything ;)

Related question: does anyone here know if it's possible to sync windows registry data across machines? Say, between a wineprefix and a real windows machine? Apparently F.I.S.H. by Fireapples (Timotainment) uses the windows registry to save your game, and I can't find a good way to sync that.

Depends. Many games from Epic have that built in. For everything else I use Nextcloud. I think most people use Syncthing.

Resilio Sync and Symlinks