Comorbid conditions are "extra problems" that go hand in hand with Aspergers.
There is still a bit of debate over whether these conditions exist separately or whether they are actually just facets or side-effects of Aspergers. Personally, I tend to favor the latter explanation for the most part although I'd agree that some of the stronger comorbids probably are stand-alone.
Comorbids can include a host of mental, adaptive and emotive disorders such as Obsessive Compulsive Disorder (OCD), Schizophrenia, Attention Deficit Hyperactive Disorder (ADHD and ADD), Depression, Anxiety, aggression, Learning disabilities and several other disorders, phobias and conditions.
Some comorbid conditions don't show themselves until adulthood and every aspie has a different combination of comorbid conditions various strengths. This is a problem which makes Aspergers difficult to diagnose. Often, one or more of the comorbid conditions is more noticeable than the others and will be picked up early. This often leads to a "wrong diagnosis" in that the comorbid is seen as the condition, rather than a symptom of Aspergers.
The delay in the Aspergers diagnosis and the effects of re-diagnosis can have a profound effect on families, social and school life. If you strongly suspect Aspergers but have received a comorbid diagnosis, you might want to seek a second opinion before accepting it.
One good thing about the comorbid conditions is that their effects can often be treated/reduced by conventional medicines in much the same way as their "sister" conditions can be treated. Medicines like Ritalin can help with ADD, while others can help with Schizophrenia, self-harm, depression and anxiety.
There is no medication that can counter the effects of aspergers - but you can certainly keep the comorbid conditions under control.