Homestuck makes many allusion to various religious and mythic traditions, but I think some are subtle or obscure enough to elude popular awareness. A couple examples:
* Everyone knows that the 69 chains of the Signless's execution became an icon of the faithful in imitation of Jesus and the cross, but his arrow wound and strung-up posture are more akin to the image of St. Sebastian, a martyr killed during one Roman persecution of the Christians.
* Feferi's trident visually cements her as princess of the sea by association with Neptune (or Aquaman, if you wanna focus on how many of the troll powers are based on cape comics), but the trident being double-sided causes it to resemble a piece of Buddhist iconography, the vajra. This is compounded by her bejeweled tiara giving her a symbolic third eye and her planet being the Land of Dew and Glass -- a Dew drop clinging to a blade of Grass is a popular Buddhist metaphor for the transience of Life, Feferi's aspect.
* There's abundant reference to the Middle East by way of Egyptian mythology, but the only explicit symbol of Islam I've seen in the story is the Rub El Hizb, a 8-point star formed by 2 overlapping squares. You can see it on the back of the playing cards in Wise Guy (630), on Jade's JUNIOR COMPU-SOOTH SPECTAGOGGLES (3158), and on Jake's SKULLTOP (4187). It blends in well with Homestuck numerous more abstract alchemical symbols.
Does anyone else have examples of religious allusions they feel have been widely overlooked?