It's definitely better to offer the clients the options, for example none free panels: direct admin, and cpanel, free panels: webmin and kloxo, in the end of the day what might seem good for you isn't really good for someone else.
You know PHP isn't only for the web and can basically accomplish anything Perl can? There are actually hundreds of languages you could use for any piece of this project.I already have a working knowledge of everything but the PHP/whatever language I'm using -> bash/running actual shell commands part. I've only screwed around with this in Perl, but logging in as another user -from- a Perl script is pretty much impossible if you're aren't running the original script as root. Is CLI any different than what Perl offers?
If you're planning on choking someone start with the people over at Piwik who insist on using command line PHP for their archiving cron...grrr. I'm in total agreement that PHP is not very efficient for command line applications.I see #!/usr/bin/php and I just want to choke someone, however. ... But, PHP has its strengths, and it should stick to those - those strengths do not lie in efficient command line application.
I use it with "off the shelf" web apps but I prefer Java, Ruby, and Python . On the command line Perl or Python.I will use it for web-based applications (that's what is was original designed for, after all).