In may not be exactly in Prague, but the All Saint's Chapel in Sedlec, a suburb of Kutna Hora, which has inspired John Connolly's The Black Angel and the film The Brothers Grimm, amongst others, can be reached from Prague's train station.
It's a 70km trip from Prague, in a warm and cosy train at a ridiculously cheap cost. Sedlec itself is an interesting place, and the ossuary in particular will leave a lasting impression with countless bones fashioned into works of art, including a chandelier which comprises of every bone in the human body! You may recognise it from books, documentaries, films or dvd's such as Ewan McGregor and Charlie Boorman's visit in their Long Way Round motorcycle world tour. Far more interesting than Paris' catacombes!
More details on directions can be found here: www.artgraphica.net/art-shop/bone-church-directions.htm
Send your feedback or queries to been.there@guardian.co.uk
Search Been there
To take photos you must buy a licence in the ossuary. It's not very expensive.
Explore the graveyard too: very beautiful headstones.
Our tour included a walk around the town and a visit to Saint Barbara Cathedral.
Tour buses leave from opposite the municipal house, or you can get picked up from your hotel.