I have a pretty broad skill set, so I face a similar problem in portfolio development.
In my portfolio, I choose to emphasize the skills that:
- I love (interaction design, prototypes, branding)
- I think will get me hired or offered jobs (marketing, analytics, mailchimp campaigns, etc.)
- Make me unique (photography, latte-making skills)
My personal website divides collections of projects into categories on the main page. I have one for personal branding (stuff I do for free for me and my friends), one for corporate branding, one for mailchimp and so on. Those are all accessible from the main page.
When actually applying for a job, I pull out the content that's most relevant to the position that I want. Sometimes that's something from every category, but often it's just one or two categories.
When the employer googles me or visits my website, they get a taste of all that I can do. Just keep in mind that when you actually send people material, you don't want to appear to be a Jack of all trades (which is why you should curate your content).
Hopefully this helps you out. If you honestly don't want to get hired for graphic design jobs, you might consider leaving them off your portfolio entirely. But, to me, that seems like a great skill that might help you get hired for a more marketing/branding type of job.