The Runaway Guys/WMG

Tim is purposely playing bad.
It's been noted that he can do complete all sorts of self-imposed challenges. However, he doesn't understand how to press A to not die, and at one point in Brawl, he spawns with Ice Climbers and simply walks off the stage. It's all because Tim is TRYING to play badly. The reason is either to lull the other guys into a false sense of security, or because he thinks he won't be able to be funny otherwise, between Chugga and Jon's rivalry.
 * That's not the reason. The reason is he's distracted by Chugga and Jon's conversations. THAT'S what makes him bad at games.

Alternatively, Tim is too busy thinking about screwing Luca/Josh/himself (take your pick) to bother to play well.
Self-explanatory.

One of the people joining the guys in the SSBB tournament will be Diabetus.
There were rumours circulating a while ago that Diabetus would be joining the guys in their next Let's Play, but he never appeared during Subspace Emissary. It could be that he was going to appear in the tournament, but not the story mode.
 * Confirmed (For Brawl!)

Every game they do an LP of will be a Mario game, or have Mario as a major character.
So far, they have played Mario Party, New Super Mario Bros. Wii, and Mario Kart 64, and their next LP is confirmed to be Mario Party 2. All of these are Mario games. They have also done Super Smash Bros., both the Nintendo 64 version and Brawl, both of which have Mario as a major character. This is likely going to be a running theme.
 * According to this formspring post, it seems like the trend will break after the Mario Power Tennis tournament.

Jon is Tsundere for Chugga
Need I even explain?

At least one of the tournament guests will come back and be a main guest a la Josh Jepson.
Why not?
 * Wobbuffet? But I think that you're on to something. Now, if it's Lucahjin...
 * If Jon and Chugga are aware of Tim's feelings for Lucah... I can already envision the results.
 * Bonus points if it's Diabetus.
 * Alternatively, Diabetus AND Quadraxis14 will be guests. Cue SNES9X jokes.

Maxwell will be a guest player on an upcoming video series.
A lot of parallels are drawn between Freelance Astronauts and The Runaway Guys, so the idea of a crossover between the two is not out of the question.

They will do an LP of Super Smash Bros 4's Adventure Mode when it comes out.
The Wii U version, naturally. And really, considering the three of them, they are going to get the Wii U. Or at least Chuggaaconroy will...

There will be another tournament with loads of other let's players again in the future, just like with SSBB.
Not only did they ask on Twitter if anybody would be interested in another tourney (as well as suggestions for possible games and guests), but really, why not?
 * Confirmed. Mario Power Tennis? HELL YEAH!

There's a different reason for Jon constantly trying to kill Chugga in New Super Mario Bros. Wii.
The given reason was that Chugga accidentally nearly gave Jon a black eye, but when you think back, they never mentioned this in the recording; when Chugga asked Jon why he was mad, Jon would just keep saying "We've been over this" like he doesn't want to talk about it. It's not that hard to say "Because you gave me a black eye", so my theory is that there's a different -- or additional -- reason for Jon's anger that they don't want to bring up, and the pillow thing was either a made-up story, or something else that happened that they put all the blame on.

NCS was playing a Zelda handheld during Subspace Emissary downtime
How else do you explain "I didn't think I got that rupee!" at the end of the game?
 * That could also explain his poor performance; his mind was on the Zelda game and not Subspace.
 * Jossed, he was playing Radiant Historia.

The next game the Guys do will be a Zelda game, likely Four Swords Adventures.
It was stated on Twitter that the next game after Mario Party 2 was chosen by Nintendo Capri Sun. Knowing him and his love for Zelda games, it's very likely he chose one. Since FSA is the only real multiplayer Zelda game (that is realistically recordable), it's a very likely choice.
 * Nope. It's Mario Power Tennis.
 * That's just a filler tournament, isn't it? FSA might be the real next game.
 * People kept asking this on Jon's formspring, and he has confirmed that it's not FSA.
 * Buth there's another The Legend of Zelda Four Swords that was re-released on the D Si...
 * How would they record the D Si?
 * Jossed anyway. Kirby's Return To Dream Land.

Jon kept getting hidden stars in MP2 through sheer force of will.
Because there are two hidden block variants: star or coin. So, if he hadn't gotten the stars, he would have gotten coins... and we all know how Jon feels about invisible coin blocks.
 * Also to make up for Pirate Land.