Did you upgrade to Wayland already? Noticed breaking stuff everywhere? One of the silent breaks is .xprofile, Wayland by design doesn't load the X legacy initialisation scripts ~/.xprofile ~/.xsession ~/.xinitrc as well as their siblings below /etc/X11. While I understand the reason to cut away legacy to forward a modern desktop environment, I'd still like GNOME to care more about helping end-users to migrate.

How to Migrate Environment Settings

If you want to set desktop global environment variables you need to task your display manager which those as Wayland explicitely refuses to provide a hook. When you use GDM a possible hook is in /usr/share/gdm/env.d/startup_${USER}.sh

How to Migrate Application Startup

The only sane way is to migrate to the autostart as defined by the XDG spec which means placing .desktop files in (usually) ~/.config/autostart. To run an arbitrary command use a shell invocation like this 
[Desktop Entry]
Name=My favourite command
GenericName=My favourite command
Comment=We all like GNOME making life harder
Exec=/bin/bash -c "ENVVAR=value my_application -o --param=value something"
Terminal=false
StartupNotify=true
Type=Application
Categories=X11;Legacy;Startup
The only relevant line being the 'Exec' entry. Use a shell with -c to pass environment variables or more complex commands.

Finally...

Maybe it is a good moment to look back at the long cross-platform compatibility ending with X11 being replaced. It was great the apply old Unix knowledge on every Linux desktop so far. Now simply stuff like xkill and xprops just won't work anymore. Don't even think about positioning windows at certain coordinates. Time to learn new Wayland-only commands.