For those new to the series and don't know where to start, the following is the production order:
("Season 1")
Bible Black: La Noche de Walpurgis - Episode 1: "School of Black Magic"
Bible Black: La Noche de Walpurgis - Episode 2: "Black Ceremony"
Bible Black: La Noche de Walpurgis - Episode 3: "Black Sacrifice"
Bible Black: La Noche de Walpurgis - Episode 4: "Black Caress"
Bible Black: Origins (La Noche de Walpurgis) - Episode 1: "Black Hallmark"
Bible Black: Origins (La Noche de Walpurgis) - Episode 2: "Black Altar"
Bible Black: La Noche de Walpurgis - Episode 5: "Black Dinner"
Bible Black: La Noche de Walpurgis - Episode 6: "Black Descent"
("Season 2")
Bible Black: New Testament (La Lanza de Longinus) - Episode 1: "Revival"
Bible Black: New Testament (La Lanza de Longinus) - Episode 2: "Reunion"
Bible Black: New Testament (La Lanza de Longinus) - Episode 3: "Rule"
Bible Black: New Testament (La Lanza de Longinus) - Episode 4: "Recollection"
Bible Black: Only Version (La Noche de Walpurgis) - Vol. 1
Bible Black: Only Version (La Noche de Walpurgis) - Vol. 2
Bible Black: New Testament (La Lanza de Longinus) - Episode 5: "Rejection"
Bible Black: New Testament (La Lanza de Longinus) - Episode 6: "Reproduction"
The "Imari Rape Scene" special for the box set I think was produced around the time of Only, but is not available uncensored. It uses BGM from both La Noche and La Lanza, which is unique since each "season" otherwise has its own particular soundtrack.
This need not be the ideal order to watch the series in, but is probably the most "safe" for beginners (no spoilers). "Only Version" can be watched before or after New Testament if you don't want to interupt that story, but Origins fits perfectly between episode 4 and 5 of the first season.