There are many factors which influence the value of a ruby. The most important one beeing it's color. Next to that there is carat, inclusions, transparancy, cut, signs of treatment(s) and color saturation.

As for any gemstone inclusions lower it's value the same is true for rubies. There is only one exception to this rule the presence of rutile silk. This type of inclusion might make the appearance of a ruby more appealing by dispersing light more evenly and thus increasing it's value. In a cabuchon cut ruby it might even cause an optic effect which is referd to as asterism. Inclusion free rubies are extremely hard to come by since they are virtually nonexistent. 

If a ruby shows signs of heat treatment (residue) it's value is almost cut in half. The more severe the treatment the less valuable a ruby will be. There are several other treatments but there is one in particular that needs to be mentioned and this is the glassfilled ruby. It's as expected a combination of ruby and lead glass. This is important because such rubies no longer posses any value since they became a manufactured product. 

Ruby is part of a larger group called corundum but is the only color of corundum to bare it's own name. All the other colors of corundum are known as (fancy) sapphires.