You're welcome. There isn't an easy yes/no answer to that. A couple things to consider. You will not be penalized by google based on who links to your site. Anyone can link to your site, and you don't control that so they are unlikely to penalize your site for others linking to you. That said, a link from a poor site might not help your rankings but instead just not play a role. You can be penalized, though, based on who your site links to. You control who your site links to, so Google does consider that relevant when considering a penalty. Don't be oversensitive with this, a small mistake will not sending your site falling if all other factors are good quality.
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if I add my company to a PHP directory and link that directory to my website, do the links in that directory give "link juice" to my site
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Potentially yes, assuming the page has pagerank and is of good quality.
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Or would I stand a chance of being penalized?
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Anytime your site links to a site associated with a "bad neighborhood" you run the chance of being penalized.
As a rule of thumb, if the site provides value to your visitors ... then link to it ... would you link to it regardless of the link juice?
I stay away from reciprocal links, personally.