1. This is the easy one: find the contact details of the website owner and ask him to remove the link. Don’t demand the other website to take the link down, but ask this politely. That usually works better
However, you will most likely also be faced with webmasters who ask you to pay for link removal or who don’t reply at all. In such cases, you should disavow the unwanted links that can’t be removed.
2. Check which low-quality pages on your website are linked by bad backlinks and get rid of the pages (404/410) instead of the links. That is probably not what you want, as most pages will have value for your website. Besides that, too many 404s send a wrong message to Google as well. In addition to getting rid of the page, you should also disavow these bad backlinks.
3. Get rid of the domain and start all over. Drastic, but if your site isn’t worth investing to clean up these bad backlinks, that might be an effective way. I wouldn’t do that unless Google has clearly penalized you for Penguin, Panda and more, though.
4. If you have just too many backlinks you want to get rid of, or webmasters aren’t responding to your call to remove the link, you can also disavow these links. That’s basically telling Google you’d prefer these links not to be taken into account when assessing your site.