How do I check with a Bash script if an application is running?

This shell script should handle the starting and stopping of any program:

#!/bin/bash

BASECMD=${1%%\ *}
PID=$(pgrep "$BASECMD")
if [ "$?" -eq "0" ]; then
    echo "at least one instance of "$BASECMD" found, killing all instances"
    kill $PID
else
    echo "no running instances of "$BASECMD" found, starting one"
    $1
 fi

let's say you saved it under ~/mystarter, you can run any command with it using ~/mystarter <name>, eg in your case, bind Meta+R to:

~/mystarter gnome-run

and make sure the script is executable: chmod u+x ~/mystarter. Also it's probably best to put it somewhere in your PATH, so you don't have to type it's full location every time.

As for the fact that gnome-run doesn't show up in ps -A, make sure that gnome run itself isn't a script that launches the actual process. Check if there is a difference between ps -A | wc -l before and after launching it (this counts all running processes).

Edit:

Since you've accepted the answer, I thought I'd add support for running commands that have commandline arguments, so that this might become a place of reference. Run a command like so:

 ./mystarter 'cmd args'

eg:

./mystarter 'ncmpcpp -c ~/.ncmpcpp'

The command just looks up ncmpcpp to see if it's running already, but executes the full command (with arguments) when ncmpcpp wasn't running.