We visited Toledo twice on day-trips several years apart and definitely left some places unexplored there even after two visits. Recognizing two millennia of history on display in Toledo, the UNESCO inscription mentions over a dozen sights by name, of which we can claim good familiarity with no more than half. The religious monuments, most importantly the cathedral and two major synagogues, have been our main targets, and we extensively explored the city on foot bypassing interiors of a number of other attractions.
At the Santa Maria la Blanca Synagogue, we found ourselves completely alone on our first visit. The space, empty of anything but mudejar columns and arches and remnants of Christian frescoes from its turn as a church, felt especially evocative without anybody else in sight.
The second time we visited the synagogue hosted an exhibition of Jewish symbolism, which somewhat dulled the impression of the great hall.
The Monastery of St John of the Kings is easier to photograph from the outside than the cathedral, which is hemmed in by the surrounding buildings in the center of the city. The monastery is located near the edge of town and is an impressive sight in its own right.
Walking uphill in the city, you come across gorgeous views of the surrounding countryside. Here is one such view with the top tier of the monastery at our eye level.
Toledo is reachable as a day-trip destination from Madrid via a speed train, a regular train or a bus, with the total one-way trip lasting between an hour and two hours, depending on which option you choose. If you intend to see all of the major religious sights, explore the army museum in Alcázar, visit El Greco home-museum in addition to viewing his masterpieces in various churches, and peek at the Roman circus, you will probably need to budget an overnight stay. Or to come back again.