Building on the answer given by Sean Connolly above, it would be very easy to imagine evolutionary scenarios where organs are more likely to develop asymmetrically than symmetrically.
For instance, imagine an organism that has a simple digestive system that consists only of a single undifferentiated intestine that runs directly from mouth to anus in a straight line, as in primitive annelids. Let's say that there is also only one enzyme present to break down the food particles, and that this is present throughout the intestine.
Now, perhaps for space issues, or for reasons that are entirely unrelated to internal organs, the intestine itself becomes asymmetrical. This could be because a longer intestine is needed to dissolve and take up more of the food, but the organism cannot become longer (for instance, it might live in dead coral reefs, and the size of the hollows cannot be controlled by the organism itself, so there is an external limitation to how long the organism can become). One way to solve this would be to fold the intestine, which can make it asymmetrical.
Now, because food particles that enter the mouth are exposed to the single enzyme throughout the intestine, the gut fluid will be less and less nutritious the farther posterior it gets along the gut. Possibly, more anterior parts of the intestine will become specialized in breaking down and absorbing more frequent kinds of food, while more posterior parts will become specialized in less common foodstuffs. This could lead to differentiation of secretory organs along the intestine, and if this is already bent because of external selection pressures, it is not impossible that a given secretory organ will develop asymmetrically simply because the intestine at the point where the enzymes secreted by this organ are to be used is not near the mid-line of the body.
For instance, if we needed to absorb substance X from our food, but substance X only became abundant in the gut fluid at a distance from the mouth that corresponds to a place when our intestine is located on the left side of the body, it is not unreasonable that development of this excretory organ would develop on the left side of the body. This could then be self-reinforcing, as a more ready access to substance X may mean that this substance becomes more important for us, and the secretory organ may become larger and more dominant, and eventually we have a large organ that exists only on the left side of the body, without ever having existed in a symmetrical form.
This is, of course, pure speculation, and I know of no example of this, but it is one that is not at odds with evolution in general, and could certainly be plausible. The same could occur if differentiation of enzyme secretion organs occur in a symmetrical gut, which later becomes asymmetrical and the whole secretory organ becomes displaced to one side. Retaining a symmetrical pair of secretory organs on each side of the body, but having the enzymes work on food only asymmetrically would imply that one of the secretory organs had a very long duct and the other had a very short one. It is reasonable to assume that over evolutionary time, the one with the long duct would become less important and may disappear.
A similar reasoning could be applied to the blood circulation system and any organs relevant to that.
There are many examples of external asymmetry throughout the animal kingdom. Many decapods, for instance, have asymmetrical claws that are used for different purposes (feeding in lobsters, for instance). Several genera of bird lice (e.g. Struthiolipeurus, Bizarrifrons) have asymmetrical heads, which probably have something to do with how they attach to their hosts' feathers. I believe that many groups of sessile invertebrates have anal openings displaced to one side, but that may be caused by internal asymmetry or because it is less efficient to have our anus situated so that feces is filtered into your mouth again.