Usually when I make a comic, I try to sneak in a movie or music reference, just for the fun of it. Since I've already done a bunch, here's a constantly updating list of what I've referenced so far:

01 - Obligatory 4th Wall Breaking:
A stab at the many, many Mega Man sprites that are out there.

02 - Suck On This!
Another stab, this time at Kirby. Also, a Batman cameo.

03 - An Urgent Call
Enter Neo. Obviously a Matrix reference.

04 - That's Not A Moon
The first comic title reference. A Star Wars one. It quotes Obi Wan Kenobi as he and some others come closer to the Death Star, which turns out to be, you guessed it, not a moon.

05 - Entering A World Of Pain
The title refers to The Big Lebowski. Neo's battlecry, “For Captain Logan!”, refers to Bill & Ted's Excellent Adventure, in which Keanu Reeves plays Ted Logan, son of Captain Logan.
Arthur's battlecry, “For Avengia!”, refers to my IRC channel, #avengia, and the comic that was based on it.

06 - Neodammerung
Named after the Matrix Revolutions soundtrack, which is played during one of the last scenes where Neo fights Agent Smith.

07 - The Empire Will Strike Back
Obviously another Star Wars reference.

08 - Requiem
Inspired by Requiem For A Dream.

09 - Foreboding
A cameo by a Doom zombie, which I put in because Doom is one of the first games I ever played on a PC.

10 - The Eve Of The War
Named after a song from Jeff Wayne's War Of The Worlds. You know, “The chances of anything coming from Mars…”

11 - Recollections From The Past
No references here. Though it's fun to mention that Randal's name is taken from one of the people that frequents #drunkduck, the DD IRC channel. Another funfact is that Abbadon is an Israelic name that means ‘Destroyer’.

12 - They Can Take Our Lives…
Obviously a Braveheart reference.

13 - Avengians, Prepare For Glory!
Both the title and the battlecries are an obvious 300 reference.

14 - Sound The Drums
The poem is something I remembered from the series Band Of Brothers. It's also used in the game Medal Of Honour.

15 - Bury The Hatchet
Taken from a Lagwagon song that goes by the same title.

16 - A Final Stand
No reference here. Excellent opportunity to tell you that Fivire's name is inspired by the band Five Iron Frenzy.

17 - Angels Are Calling
Inspired by the title of an Insane Clown Posse song, ‘Angels Are Falling’.

18 - Look Into My Mind, Tell Me What You See
No reference here. Gives me the chance to tell you that Neo's, or Creatos', tombstone was taken from a Doom sprite-sheet, as well as the tree Grak is hiding behind in an earlier episode.
The backgrounds are generally taken from a Halo game, except the Throne Room background, which was taken from Phantasy Star IV.

19 - With Great Power…
…Comes great responsibility. It's a Spider-Man reference.

20 - If Knowledge Is Power…
A quote from Batman Forever, as spoken by the Riddler: "For if knowledge is power, then a God…am…I."

21 - The Thing That Should Not Be
Taken from a Metallica song that goes by the same title.

22 - Should Old Aquaintaince Be Forgot
A line from ‘Auld Lang Syne’.

23 - Great Scott!
A reference to Back To The Future, where Doc Brown repeatedly used the phrase. There's more BTTF references in here, check the Translation Thread for that.

24 - We Were Somewhere Around Barstow
Opening lines to Fear & Loathing In Las Vegas.

25 - Resistance Is Futile
Obvious Star Trek reference.

26 - I Come From A Land Down Under
Taken from the song ‘Land Down Under’ by Men At Work, in which the singer asks a man from Brussels, “Do you speak-a my language?”

27 - Hollow Forces
Combination of Hollow Man' and the title of an Aquabats song, named ‘Awesome Forces’.

28 - The Sorcerers Apprentice
Reference to the Mickey Mouse short from Fantasia.

29 - A-traveling In The More
It's the sentence Arthur was singing when he interrupted himself.

30 - Happy Landings
No reference here, just a nice cliffhanger.

31 - He Lives To Die Another Day
A James Bond reference.

32 - First Blood
A Rambo reference.

33 - Combo Breaker
A phrase used in a bunch of videogames.

34 - Simplicity Undone
No reference to see here, move along.

35 - Return To Sender
Taken from the title of an Elvis song.

36 - Come With Me If You Want To Live
A Terminator reference.

37 - Punishment
No reference to see here, move along.

38 - And When I Get That Feeling
Taken from the lyrics of ‘Sexual Healing’ by Marvin Gaye.

I KNEW that was a Lagwagon reference! Also, kudos for your love of the Aquabats.

Yay kudos. Also, I didn't think anyone listened to Lagwagon anymore! Kudos for knowing Lagwagon!

KUDOS FOR KUDOING!
…
i just wanted to be apart of this conversation.

It's ok, we still love you, even though we don't show it.

Yay Lagwagon! My roommate in college was a big fan, so she got me hooked - we used to go see them in Houston.

I actually saw them not too long ago. It was awesome. I got a shirt :3