The Scratchware - the "security app" Xefros downloaded in the beginning of his part of the game - is an obvious reference to the cueball, as well.

additionally with the portal itself there are two snakes with red and green eyes, probably referring to cherub reproduction. the dates in joey's diary are all the significant numbers in HS (413, 612, 1025)

A real obvious one but a very nice touch
When Joey asks what Xefros is rebelling against she says "The man?" and that text specifically is in green with a white for the a.

Something i noted was the painting of the dragon-like creatures in the hallway in Half-Harley Manor next to the closet. The big white one has LE stripes on it.
Pretty sure its supposed to be LE, HIC and The Handmaid.

And remember the "ceratain omniscient cueball" prefers to talk to young women

dammak?

The statue on the stairs isn't a denizen relating to Homestuck but there is a mounted Typheus in the basement.
Joey has a Manthro Chap on a beanbag in her room just like the one Jade plays with in Act 3. Interacting with it gives you a reference to Andrew's Humanimals comics and the "What a daring dream!" spiel also from Act 3.
Next to the LE!Castle Grayskull toy by the stairs there are pink Ninja Turtle toys alluding to the LOLAR consorts.
The dog shaped crests and one of the Lite Brite images are of Halley, Grandpa Harley's old guardian dog.
Arena Stickball is based on "Table Stickball", a game The Felt claim they made up based on their hats (which was just pool). The balls in Arena Stickball have powers that match their corresponding Felt members.
Slothdad's canon name Zoosmell is a reference Humanimals and the second page of Homestuck.

I'm sure there's way more but that's all I remember.

Have you looked at the stopped clock in the trophy room and the number on top of the portal, and how the same number constantly repeats itself throughout Homestuck?

The number 11 shows up so often because it represents synchronicity. People in completely different places, working at the same time to achieve the same goal. This concept completely opposes how Doc Scratch keeps trying to be the cause of everything. I am slightly dissapointed in the Homestuck wiki editors for not realizing this~

One detail that caught my attention was using the batteries on the shelf filled with stuffed animals back in Joey's room. Remember how Jake forces Jade to carry a loaded firearm at all times?

Have you tried using the ballerina slippers on the poster of Acorn's Shadow over in Joey's room? Yin & Yang imagery was a major part of Homestuck. Carapacians and Cherbs. Just and Heroic. Twin moons of light and dark, orbiting a planet awaiting rebirth.

Have you noticed a hint of wanderlust in Joey's personality? From looking around Joey's room I noticed that she has some rather estoric tastes. The symbol on her shirt is a compass rose. In Homestuck the four kids eventually inherited some of their parent's personality traits despite their best efforts to avoid this. Might this repeat itself with Joey and her vagabond parents?

When you use the heirloom on some items it will give you background into Joey's life, such as how it wasn't her mother who gave her the heirloom but rather she found it in her mother's jewelry box and assumed her mother wanted her to have it. The jewelry box can be seen to move whenever you enter the room and the key itself also exhibits strange tendencies when used on other items and of course when Joey is forced to open the portal.

Homestuck spoilers below:

Based on my knowledge of Homestuck and how in post-scratch Alternia "a certain omniscient cueball" actuvely played a part in putting certain events into action to prep Alternia for the game and the summoning of Lord English, my guess is that he is controlling Joey and Xefros into putting a new Empress in-charge and other such things to contribute to his preperation of Alternia for the later events of Homestuck (such as possibly planting the key/heirloom himself).