Here comes a long review!
First of all, I think it's fine that you made one just for your shorts. A flash movie is a flash movie. The animation was good. I mean, I know you could have done better but I'd give it a pass for good; I can't say I can do any better. But well... here's the thing.
The majority of your parts are lacking in humour. A lot of the jokes gave me the feel that you were trying too hard. What I mean is that skits would be drawn out; characters would comment about the jokes, basically nullifying them; small and sometimes larger bits would be added into skits where they should have ended which subtracted from the humour rather than contributing to it... Then there were the ones that were just plain unfunny, due to either a bad idea or a poor joke execution. I think the biggest mistake you made had to do with focusing on throwing in as many Sonic related elements as you could rather than focusing on the quality of the jokes. Don't get me wrong, I understood probably 80 - 90% of the jokes. Hmm... there's a lot to cover so let's do some analysis.
Eggman Amusement Park: Too long, many jokes felt forced. However, the way "filled with candy" was pronounced kind of made me laugh inside. I guess that part was pretty unexpected too so that was probably a big part of it.
Tornado Jump: Nothing too funny here. "That was awesome" isn't a good punchline if you ask me. I've heard it before in other collab skits and I didn't find those funny either... not to mention that you could plainly see that Sonic was enjoying himself during the whole thing.
Bubble Spikes: May have had potential, however I didn't care for the execution.
Cute Couple: I didn't like this one much at all. It would have been significantly better if you cut it before Amy's "they're a cute couple?!" and even then, it still wouldn't be one of my favourites.
Guy Gets Wrongly Arrested: I have never liked Sonic X or really watched a lot of it, but I can tell that even if I did get the idea, I still wouldn't find this one funny.
Knuckles and Lever: Would have been much better off without Knuckles' "whatever you say" line. Then again it would still just be your average slapstick gag.
Sonic Michael Jackson: Short and sweet. Made me laugh.
Metal Sonic: I didn't like the joke. As predictable as the whole thing is, if you HAD to use it I would have cut it after Sonic's facepalm. The part where Shadow says "I can relate" is one of the things I was referring to when I mentioned how you were throwing in Sonic elements. Maybe a hardcore Sonic fanboy might laugh at something like that but I can't say I ever would.
Electric Field: Meh.
Crab Claw: Meh.
Team Rose: Good concept I suppose. It wasn't funny to me though. It felt too long but it wouldn't be easy to get the joke in if it were any shorter. Kind of a dud idea I guess.
Some Joke Involving the OVA: The whole idea just seemed stupid. It feels like it's been done a million times in other forms.
Burning Dinosaur Robot Thing: Seems like a dark joke without the gore. People who like dark jokes won't find it funny and neither will people that don't. You might get the inbetweeners I guess.
Blaze Doing Pirouettes or Whatever: Meh.
Fire Field: Felt like you thought of this in a minute. Meh.
Real Life Chaotix: Heh. Made me smile.
Chao Halo: The joke implies that the halo looks like a doughnut. It's round with a hole in it but there's not much else that really likens them to eachother so it felt like a forced joke.
Eggman Blows Up the Earth: Eggman didn't think his whole plan through. Nothing much to see here.
Food Thing: This has to be my least favourite. It was the most drawn out of all and had way too many parts that I felt it could have done without. I didn't find any of it funny either. The whole idea was generally bad if you ask me.
Well, yeah. I apologize if I may seem a bit harsh. I see a lot of effort put into this. Maybe you were targeting this at hardcore Sonic fans. However, I hope you take this to heart. I've made many of the same comedy mistakes in the past and have learned from them. Good luck in future projects. :)