As you probably know white vinegar is not the best for your anti-candida diet, if you're not sure why, you should visit http://candidaquestions.probacto.com/170/can-i-have-vinegar-while-im-treating-myself-for-candida. I give a pretty brief explanation on what should be changed and fixed with white vinegar in general.
Apple cider vinegar, or ACV, on the other hand, is commonly recommended for those who are following an anti-candida diet protocol. The trick is to make sure you are using an unfiltered, raw, with the 'mother' apple cider vinegar. This means that it is completely unpasteurized, and they generally have about 5% acidity. It needs to be made from organic apples as well. You can usually find this in health food stores or in grocery stores that have a health food section, Bragg is the most common brand by far, and can be found easily, but do not always discredit other brands.
Believe it or not, the best natural ACV will have a cloudy appearance. The only reason the regular processed varieties don’t look cloudy is just that – they’ve been processed to make it “look better” so that you’ll be less wary of buying it. The lack of processing ensures higher levels of lactic acid, which is where most of the true benefit lies. I do shake the apple cider vinegar before I use it to make sure it's mixed around properly.
ACV isn’t always ingested but is very often used for vaginal douches when women are suffering from vaginal thrush and system infections. If in doubt, avoid all forms of vinegar. If you do give ACV a try, monitor your progress to make sure it’s not setting you back. And, as always, talk to your naturopath or physician if you aren’t sure what to do.