Commuting is time you wouldn't spend if you didn't have this specific job. It's not leisure time you control, so many people find it useful to count it when comparing how much of their life a job actually costs.
Either works as long as you're consistent — gross salary gives your real hourly wage before tax, net salary gives it after tax. Use whichever you want to compare against.
Use it to compare job offers more honestly (a higher salary with a brutal commute may pay less per hour of your life than a lower salary close to home), or to decide if a side project, freelance rate, or different job is actually worth your time.