Check the pinned comment for a full list of timestamps, written by the great Christopher Moon, thank you so much to them!!!
I also have a playlist with most of the songs if you want to check it out:    • Every Toby Fox Song  

The songs are in the "general" order that they came out in (with a few exceptions), but the exact order isn't correct.

Here are just a few interesting things that I found:
-The song "Man" from Deltarune (11:23:25) is actually a different version of a part of a song that Toby released on his Tumblr before Undertale even released (3:42:33)!

-The song "The Holy" from Deltarune (11:15:37) is actually based on a song called "Treasure Hunter" from Toby's website. (6:37:08) which also came out before Undertale.

-Toby Fox has a few melodies that appear throughout all of his work, even work that seemingly isn't connected to eachother. For example, the main melody that appears in "Nightmare Knight" (6:35:19), also appears in "Friendship" (6:27:35), "You Know What This Is" (6:37:50), "The Door" (10:45:08), and "The Chase" (10:46:38).
There are also many more examples, which I would list but I am going to reach the character limit soon.

Here are some things to note about the video itself:

I only included stuff that I considered "songs" or at least "jingles". This means that ambient tracks such as "Weird Birds" from Deltarune or "Long Elevator" from Undertale aren't featured in this video.

I decided not to include tracks which are just covers of other tracks, such as Toby's piano cover of the My Little Pony theme, his remix of the Seinfeld theme with the Megaman Soundfont, or his Undertale 5th anniversary piano medley.
The Earthbound Halloween Hack soundtrack (which are mostly just edits of the original Earthbound music) is the only exception to this, as I'm fairly sure that it's the first music that Toby released, so it only felt right to include.
I will admit that I was fairly inconsistent with this rule though, and a few remixes may have made it into the final video, particuarly remixes from the Homestuck Sound Test.

There's some old Toby Fox music uploaded on Tumblr that can no longer be accessed, even through the Wayback Machine. This unfortunately means that I couldn't include them in my video. As far as I know, though, those are the only Toby Fox songs that aren't in the video. There's a good chance that I missed a few more on top of that though, so please tell me if I did, and I will update the description accordingly. Also this video was made before Deltarune Chapter 2 so it isn't included.

-I did make a few editing mistakes in this video. For example, at 3:36:26, the song is named "Improved Touhou Music with Annoying Commentary". It should instead say "IMPROVISED Touhou Music with Annoying Commentary". Another typo is the fact that I labelled "Lost Girl [Version 2]" as being from Dweller's Empty Path, when it's obviously from Deltarune Chapter 2.
Also, at at 14:36:30, the "Ralsei's Lullaby" jingle is supposed to playing. However, for some reason, there is no sound in that part of the video. I think that might be a rendering error.
Also also, I accidentally included Papyrus's Cool Song twice! But it's fine because Papyrus deserves it 💙
There are a few more typos like this considering I had to write titles for nearly 600 songs, but I don't think anybody really cares for a full list of mistakes.

-The three songs at around 4:20:00 (Indigo Heir, Rust Maid, and the Brave and the Bronze) and NOT by Toby Fox. I don't know how they snuck their way into this video.

CHAPTERS:
00:00 - Intro
0:00:12 - Earthbound Halloween Hack OST
00:15:26 - Midnight Crew: Drawing Dead
00:19:00 - Homestuck Vol. 4
00:26:40 - Homestuck Vol. 5
00:59:00 - Alternia
1:33:12 - Squiddles!
1:35:06 - The Felt
1:40:47 - Homestuck Vol. 6
1:57:30 - Alterniabound
2:24:27 - Fwugradiation YouTube Channel
2:28:15 - At the Prince of Oblivion
2:35:43 - The Wanderers
2:45:00 - Homestuck Vol. 7
2:57:30 - I Miss You (Earthbound 2012)
3:06:30 - Colours and Mayhem
3:07:34 - Homestuck Vol. 9
3:20:44 - The Baby is You 😳
3:34:45 - Toby Fox Tumblr
4:06:12 - Fwugraditaion YouTube Channel (Again!)
4:13:17 - Starbound Beta
4:15:25 - Kiwi Blast
4:17:45 - Homestuck Sound Test Songs
6:16:28 - Toby Fox Website
6:39:09 - Homestuck: Home for the Holidays
6:40:45 - Cherbium
6:43:42 - Undertale (Of Course...)
9:21:33 - Make Music, Throw Music
9:27:23 - Potion Shop
9:31:55 - YIIK
9:34:53 - Omori
9:36:25 - Rose of Winter
9:40:43 - [S] Collide
9:46:21 - Homestuck Act 7
9:55:20 - Hiveswap
10:30:25 - Misc Homestuck Songs
10:41:32 - Deltarune
11:28:20 - Dweller's Empty Path
12:41:04 - Escaped Chasm
12:45:45 - Pesterquest
12:47:53 - Little Town Hero
14:25:31 - Smash Ultimate
14:30:27 - Pokemon Sword and Shield
14:32:53 - PRAY

Sad annoying dog sprite by lykaspars
Minecraft Toby Fox Image by u/JimmyShow124