In the Panteón de Reyes, we can find:
* Carlos I and V and his wife Isabel de Portugal .
* Felipe II and his fourth wife, Ana de Austria.
* Felipe III and his wife Margarita de Austria.
* Felipe IV and his two wives, Isabel de Borbón and Mariana de Austria.
* Carlos II.
* Luis I and his mother, María Luisa de Saboya.
* Carlos III and his wife, María Amalia de Sajonia.
* Carlos IV and his wife, María Luisa de Parma.
* Fernando VII and his fourth wife, María Cristina de Borbón.
* Isabel II and her husband, Francisco de Asís de Borbón.
* Alfonso XII and his second wife María Cristina de Habsburgo-Lorena.
* Alfonso XIII and his wife, Victoria Eugenia of Battemberg.
* Don Juan, count of Barcelona, and his wife, María de Borbón.
In the Panteón de Infantes we can find the queens that didn't have reigning children and other members of the Royal Family.
In the Panteón de Niños we can find the royal princes and princesses that died in infancy, interred in a magnificent common tomb that has the shape of a birthday cake.
I'll try to name some members of the royal family buried in the Panteón de Infantes, lets see if I don't get mistaken:
Of Juana la Loca and Felipe's children: María, Dowager Queen of Hungary and Leonor, Dowager Queen of France.
Of Carlos I's children: Fernando (1529-1530), Juan (1537-1538), in the Panteón de Niños, and don Juan de Austria (1547-1578), his bastard son, in the Panteón de Infantes.
Of Felipe II's times: don Carlos (1545-1568), Isabel de Valois (1546-1568), their last daughter (b. and d. in 1568); his other children: Fernando (1571-1578), Carlos Lorenzo (1573-1575), Diego (1575-1582) and María (1580-1583).
Of Felipe III's times: his children María (1603-1603), Carlos (1607-1632), Margarita (1610-1617) and Alfonso (1611-1612) are certainly there. I am not sure about Fernando (1609-1641), he died in Brussels, but I think his corpse was sent to Spain, so he is very possibly buried in El Escorial.
Of Felipe IV's times: his children Margarita María (1621-1621), Margarita María Catalina (1623-1623), María Eugenia (1625-1627), Isabel (1627-1627), Baltasar Carlos (1629-1646), María Antonia (1635-1637), María Ambrosia (1655-1655), a stillborn daughter (1656), Felipe Próspero (1657-1661), Fernando (1658-1659) and his two of his bastard sons: Francisco Fernando (1626-1634) and don Juan José (1629-1679).
Of Carlos II's times: his two wives, Marie Louise d'Orléans (1662-1689) and Maria Anna von Neuburg (1667-1740).
I think that's it for the Austrias, I'll post about the Bourbons tomorrow!