Conventional wisdom says, when designing a kitchen, the stone selection should come first. (...followed by flooring, cabinet finishes, fabric, wall color, and accents--in that order) The reason for this is that the stone is the most permanent and the most limiting--you can't just create an image of the stone in your head and then go find it--or have a magazine picture or sample in hand and scout out a replica. So, if you are starting from scratch (lucky you) go out and find a natural stone you love and build your kitchen around it.
But for the rest of us (the vast majority), our kitchens will only be getting an update. Many homeowners planning a kitchen remodel will be replacing appliances, hardware, and countertops. The existing cabinets, and often the flooring, will not change.
Lets look at a case study.

Here is a typical 20-year-old kitchen. It has good quality honey oak cabinets and "pinky-beige" ceramic tile underfoot. Honey oak wood lends itself nicely to a simple, country look with plain, light-colored countertops (which just happened to be the rage, 20 years ago) The problem is, many homeowners today are attracted to some of the current, colorful and exotic granite now available. But, unfortunately, just because you love a stone, doesn't mean it will look good in your kitchen. (It works sort of like loving a hair style, or a bathing suit)
Time to make a plan for the remodel.
Option #1: Paint the cabinets white and choose a granite that relates to the pink undertones in the floor. There are many great choices that would work here. In this case, there can be as much movement as you'd like because you aren't competing with any wood grain. Or you can go with an understated look of darker stone with a more even pattern, as long as it relates to the floor color--such as the Marrom Cahiba below, which is a deep plum.
Some examples:

Flemingo Mantegna Typhoon Bordeaux

Marrom Cahiba Succuri Four Seasons
(Remember, don't set your heart on a photo---you'll never be able to find an exact match!)
Option #2: If you intend to leave the original honey oak finish on the cabinets, the stone selection will need to relate to both the floor color and the cabinet color. The stone now needs to pull together the pink in the floor and the yellow/gold of the wood. Obviously, you will need to eliminate any stone that clashes with one color or the other. Many color schemes that go well with gold will look terrible with pink (and visa verse) Another important thing to consider is this: you must be very careful when combining the grainy look of oak with the movement of an exotic granite. You may end up with a kitchen that makes your head spin. The phrase "busy kitchen" doesn't necessarily mean that there's a lot of cooking going on!
Here are some possibilities for the kitchen that is retaining both the golden oak cabinets and the pink/beige floor:

AfricanIvory Almond Mauve Crema Bordeaux

Juperana Florence Niagra Gold Starburst
Option #3: You may decide to keep the oak, but spring for a new floor made from mid-toned wood or cork. (If you choose this option, it may be a good time to tweak the layout of the cabinets, while you are at it) When selecting a stone for this option, choose something with at least a little gold in it. The honey oak will bring out the gold in the stone and tie the two elements together. (Soapstone is an exception--it works like a neutral and looks good with pretty much whatever you put with it!) The examples below may work for you, depending on the other colors in your home:

Cafe Imperial Juperana Giovota Ouro Romano

Fire 'n Ice Golden Eye Soapstone
(By the way, always keep in mind the flow of colors from one room to another. It is okay to emphasize different colors in different rooms, but it looks best when they all belong to an interrelated color scheme. In my opinion, it is most desirable to have all the rooms relate to one another, as though they all belong in the same house--which they do!)