Thanks for your thoughts on this!

Licenses are not an issue, they're in BaseDirectory already anyway.

I don't use a lot of LibraryLink stuff, but that's a good point to keep in mind.

Likewise, Paclets are something I mostly use unknowingly, that is, only when Mathematica uses them behind the scenes. I know you recently transitioned some of your packages to paclets, but I haven't looked into the pros and cons of that for myself. Good point though on the config files, I'd really have to ensure that my Dropbox folder is in the same location on all computers.

It's reassuring that you don't expect problems with items 3 and 4; those would be a real pain to mitigate.

At the moment I'm syncing Applications, Kernel (have a few lines of stuff in the init.m), and SystemFiles/Formats (recently started transitioning my import/export packages to registered import/export types and prefer the simplicity of that). However, just looking at some of the other directories: SystemFiles/FrontEnd is also a syncing candidate (I don't use palettes much, but that could always change). ApplicationData is another folder that I might actually use for its intended purpose of storing configurations and preferences for packages, with the obvious caveat that these are things I may want to set differently on different computers.

On the other hand, sharing packages with other people is obviously a lot easier if the contents that need to be installed are limited to the Applications folder; that's something many people will already know about, so an installation script wouldn't be necessary.

Still undecided... Knowing myself, I'll end up trying this at some point just for the fun of it, but realistically I'm probably better off selectively syncing. I'll certainly report back if I do try it though!