Alt+F2 (Run Application) doesn't work for custom commands

I assume the bashrc is not read by Gnome, and why should it, since it is a config file for bash.

I define my path in ~/.profile. This file is definitely read by the Gnome and XFCE environments and should by others as well. (But it is read only on login, so you have to log out and back in any the changes to take effect!)

~/.bashrc is included by ~/.profile by default. The ~/bin directory is added to PATH by default too. Create the ~/bin directory and add sym-links (ln -s) to applications you intent to use, or modify your ~/.bashrc.

The default content of the mentioned files can be found in /etc/skel -- used while creating new account and their home directories.