Over here: Lesson 3: You want a web portfolio? For a programmer?":

"I get it. PHP is largely used in the construction of websites so any PHP developer must have a portfolio ready to go, right? Wrong. If I pointed you to any of the websites I've worked on the likelyhood that you'd be judging me on a graphic designer's skillset rather than my own is fairly high."

I've not really thought much about this as I don't have much in the way of a portfolio that is visible to the general public, but it seems blindingly obvious on reflection. 

When I've worked on a site's CMS, potential clients are typically not going to know or care much about that side of it.  In fact, if it's done properly, they shouldn't be able to tell a CMS is driving the site.  They will instead be evaluating the site's design and general user experience, which will reflect more on the abilities of the designers and information architects than on anything I have done.  Moreover, once a CMS-based site has been left in the hands of the site owner for a while, their content will also become a factor that contributes to the overall impression of the site.

Ideally, a potential client would be able to see the back end of the site to evaluate the real CMS functionality.  But this is not really feasible or suitable for a number of reasons.

As the article suggests, a code sample would be appropriate, or a link to an openly available project.  But you would really need to be a programmer yourself accurately to evaluate this.

It seems that what you are left with is reference sites.  I can claim that 'I wrote the e-commerce engine for site X' or 'I built the CMS for site Y', and impress upon the potential client that I am a developer and not a designer.  How this is best done is a different matter.