In the Cellar after you get Klaus across the goo (which is drained by Violet), you must find a way to get Violet across. You cannot clear out all the rats. You must run past all the rats and find a wheel. When you do, press B. The pathway will fill up. Then, use Violet's "Steady Stilts" to get her across. Note: Watch out for the steam pipes.
Health Lockets
When climbing on the outside of Count Olaf's Tower, you usually go to the left to work your way up the tower. However, sometimes if you work your way to the right and peek around corners you might not normally look, you can find health lockets.
Hidden extras
Collect all 125 hidden puzzle pieces.
Klaus
Klaus has a ability to do more with flying with Violet's invention. Use Klaus for that to fly over things.
Levitating Loafers For Klaus
At Uncle Monty's house you will need to make a pair of Levitating Loafers for Klaus. You will find one of the invention pieces, a pair of boots, outside the shed, above the door, in Uncle Monty's garden. In order to climb up and get the boots, you will need to use the Brilliant Bopper (or the Fruit Flinger) to knock over the water cans that hang from the second floor windows. The spilled water will cause giant flowers to grow. You can then jump on these to get over to the roof and grab the boots.
Making the Fruitflinger
Go to the West Hall. There is an enemy at the corner. With Klaus, go to the wall and wait, then hit her. Go to the cabinet and push it. Go in the secret room. On the way to the piano in the main room, there is fan. Take it. Then, go to the kitchen . Another enemy is there. He will throw three meatballs at you. After he throws them at you, run up to him and hit him. Repeat the process until you win.
Protect Aunt Josephine from Leeches
Aim your peppermint popper closely in front of her feet. Once it is aimed properly, do not stop firing it. This should work for all the Leeches.
Get Violet across the rats...