A lot of fun, but still has room for improvement
This is a great little collection of video game bloopers, and definitely worth watching if you're in need of a chuckle. I think the fairest way to break this down is by scene. Incidentally, I must say I love your scene selection screen. I happen to be a huge Mega Man fan, so I appreciate that you came up with the idea of modifying the stage selection screen to allow the viewer to pick a particular clip in the movie, complete with the music from the game and all. The pictures for each scene make it relatively easy to locate whichever one you need, and I like how the pictures change to the scene numbers as you hover your mouse over them. Now, on to the actual scenes!
Scene 1: The first thing I noticed about this one is the One-Up Mushroom noise that could be heard as the text appeared over Mario's head. I thought it added a really nice touch, in the sense that it just helped set the mood of being in the Mushroom Kingdom. However, the punchline feels a bit bland, and might have been funnier if Mario could perhaps be seen struggling in the lava as he bursts into flame.
Scene 2: Loved it, with Mega Man running while the overly dramatic track played in the background. I never would have made the connection that it looks like Dr. Light is searching for a contact lens, I thought that was brilliant! The only problem with this one is that the text is a bit difficult to read against the background.
Scene 3: Ah, the wonder of fart jokes. The only thing better than a fart joke is a grotesquely exaggerated fart joke. Which is why I think this would have been funnier with a longer, louder fart. It would have been great if the fart had ignited some of those bushes, too.
Scene 4: I noticed that the horizontal part of the pipe on the bottom-left is slightly misaligned with the vertical part. Otherwise, this is one of the best scenes in the whole movie. I thought the joke would be over after Mario was launched into the air, so I love how you surprised me by continuing it and having the pipe fire him into the side of the castle. The fireworks were just the icing on a beautifully made cake.
Scene 5: I think you must have mis-credited the music from this scene. Although the background is indeed Heat Man's level from Mega Man 2, the music is from Fire Man's stage in the first Mega Man game. The credits say that you used music from Mega Man 2, but I did not hear any tracks from that game. And there was not a credit for the music from the first Mega Man. I can only assume that there was a little mix-up somewhere along the line. The scene itself, however, is fine, and I particularly like the little "sproing" noise when Mega Man jumps on the Rush Coil. The underwater theme from Super Mario Bros. works surprisingly well in space.
Scene 6: Haha, I've always wanted to say something along those lines to that fairy, even if she is really a kindred spirit. The red "HEY! FATSO!" text was a bit difficult to read, although the white text caused me no trouble. Both of the voice clips here were pretty hilarious. The only other problem is that after Link runs away, you can still see his cap moving at the bottom of the screen.
Scene 7: I don't have much to say about this scene, beyond that I like how Mario curses right before the Fat Chocobo lands on his head.
Scene 8: Thankfully, the text in this one is a bit easier to read against the background. You also cut the music off at the perfect moment for comedic effect. Did you custom-sprite Mega Man pointing for the part where he laughs? Because it looks pretty good.
Scene 9: I see that you saved the best for last, or so I feel. While all the other scenes were definitely worth a hearty chuckle, this was the one that really got me laughing. Once again, the red text was a bit difficult to read, particularly where it says "Master Sword!" But you more than made up for it when Link got fried by the lightning, that was pure genius!
In summary, this animation contains all-around good sprite work, although the quality on some of those sound clips could have been better. Nice work, I'd like to see more of these!