Apo (ap, aph), from; apogee, apology, apostrophe, aphelion, aphorism.
Cata, down; catarrh, catalepsy, catastrophe, catechism, cathartic, cathedral, catalogue.
Di (dis), two; diphthong, dissyllable, dilemma, diploma.
Dia, through; diameter, diagonal, diaphonous, diabolic, diagnosis, diastole, diaphragm.
En (el, em), in; ellipse, emblem, energy, enthrone, empyrean, emphasis, emporium.
Endo, within; endogenous.
Epi (ep), upon; epilogue, epitaph, epiphany, epistle.
Exo, without; exogenous, exotic.
Hyper, over or above; hyperbola, hyperbole, hyperbolical, hypercritical, hyperborean.
Hypo (hyph), under; hypotenuse, hypothesis, hypocrite, hyphen.