I've rewatched the episode and the audience laughs when:

- Sheldon yawns
- Sheldon looks forward with a weird expression
- Sheldon is mixing the cereal with the milk and walking

In my opinion, the audience laughs because: 

- Sheldon faces and expressions
- Sheldon is kind of sleepy and grumpy
- The fact that Sheldon has some kind of morning routine
- The scene is too quiet and they added the laughs.
- I also think some of the laughs are from people seeing Leonard on the couch before us viewers.

I also chuckled a little bit during the scene before I knew Leonard was in the couch, Sheldon is just humorous...