Before I say anything else - GUNNERPOW, I hope you didn't skip the intermission after Act 3! It's important (or at least interesting) later on. Maybe you'll come back and read it again when you realize that. I know I did. :3
Great topic. I just can't answer it without listing a thousand songs xD But those I like the most are the classic ones that just set the tone for Homestuck and have inspired many later songs. George Buzinkai is probably my favorite Homestuck composer.
Here follows my favorite Homestuck songs and where they were used in case they were used. Oldest to newest:
Three in the Morning - Used when we first see Sn0wman. Several remixes of this jazzlike song have been made and it just fits in with the Midnight Crew and the Felt so well.
Remixes include: 3 In The Morning (Pianokind)
Skies of Skaia - pure beauty. First used when Nanna tells the story of Skaia's battle.
Nice remixes: Song of Skaia, Skaia (Incipishpere remix)
Ballad of Awakening - this song isn't used again from what I remember, but the deep feeling it provides when it is used in the flash where we see Jade dreaming just adds so much to the epicness that you begin to understand that Homestuck is.
Sburban Jungle - yes of course. This made Rose's entrance to the Medium thrilling. It's been used again as part of many songs and drastically remixed in Another Jungle.
DOCTOR - this is my absolute favorite of all Homestuck songs. Hands down. Its remixes are more epic, sure, but this first played when John got to see what his Land was really like and this melody just IS Homestuck for me. Perhaps the most remixed song? There are a ton of less notable remixes, and then there are two special songs where Doctor has been merged with Penumbra Phantasm, a song which has never been completely revealed... Savior of the Waking World, Savior of the Dreaming Dead
Other, more pure remixes can be found on Homestuck Vol.5 but here is one jewel: Green Ghost
Descend - this is an end-of-act flash song which consists of several different tunes. First we have the obvious Upward Movement (Dave Owns), then suddenly we have the melody from Beatdown (Strider Style) and switch into the theme of Black (which in turn is a remix of Liquid Negrocity). All in all, this theme is fantastic, as is its flash clip.
Other remixes of Upward Movement: Terezi Owns, Rize of the Denizens (unofficial but great!)
Temporal Piano - probably a remix of Temporary, or the other way around?. Too beautiful for the Felt, makes you think about what a hard life LE's servants must lead...
Gaia Queen - made for Jade, but never used in a flash. I really love it and it fits well together with the flash where Jade enters the Medium!
Crystalanthology - a feelfull remix of Crystalanthemums, a song that has been incorporated and remixed in many ways. It probably has something to do with Vriska, as she is featured in the images. Only remix used in a flash is Crystalmanthequins, which shows us a bit from the trolls' history and session.
Other notable remix: Crystalmethequins
Even in Death - mystic and strange. Maybe made for grimdark Rose but used when Roxy sleepwalks. Its remix was used to show us a bit of the alpha kids' session.
Remix: Even in Death (T'Morra's Belly Mix)
Calamity - nothing special, never used to my knowledge but still great!
Galaxy Hearts - a really nice tune. Never used, but the feeling it gives off is really nice. Kind of hopeless and mystic at the same time.
Infinity Mechanism - the artist thought about the gravity of the Scratch when they painted the image, and I'm not sure about what the composer thought. But it was used to foreshadow events in the alpha session and give us a feeling of starting off fresh, a new chance, a new Skaia! I really love the epic restart feeling that it gives off. A personal top favorite.
Moonsetter - because it's to pleasant and sad at once, especially when you look at the picture. Never used, but cute.
A Taste for Adventure - it is epic. It fits with the Cascade flash animation! I really hope Hussie makes a flash to this music one day. It would be amazing.