If your jars contain classes that are all in the same package(s), you can use the form with "<includeClasses regex=..." (note: try regular glob patterns before you try regex, in my experience).
You can pass a war file, and it will instrument the classes from the pattern in any jar within WEB-INF/lib (or classes within WEB-INF/classes).
<cob:cobertura-instrument datafile="${todir}/${instrument.ser.filename}" >
<includeClasses regex="com.mycompany.*" />
<instrumentationClasspath>
<pathelement path="${war.file}"/>
</instrumentationClasspath>
</cob:cobertura-instrument>
Alternatively, if you really need to pinpoint specific jars within WEB-INF/lib/ folder, you can try the form with ant zip/jar filesets (I haven't tried it):
<cob:cobertura-instrument datafile="${todir}/${instrument.ser.filename}" >
<zipfileset src="${war.file}" includes="WEB-INF/lib/com.mycompany*.jar"/>
</cob:cobertura-instrument>
If all else fails, I would do what you probalby have considered: extract these jars, instrument them (with the first form) and re-package them.