Inside Jokes

An Inside Joke is some kind of gag reappears throughout several Episodes, which might not be obvious to all viewers. Here are some Inside Jokes that people who are new to Space tree would not get. In fact, some of us who have seen most of the episodes may not have fully picked up on them.
Link to Inside Jokes on the old Wiki: https://web.archive.org/web/20111204233741/http://stwiki.coramaximus.com/Inside_Jokes
Inside Jokes
"You had the power within you the whole time"
Doodles
Episodes ending in laughter
Fake Beards
Hyperdrive Stasis
I'm a busy bee
IMs
It sure is.
Jumping Through Windows
Mugs
OR AM I?/OR IS IT?
Philip Seymour Horseman
Signing of letters with "love"
Smoking Pipe
Space Tree's Italian Ancestry
Space Tree's Sunglasses
Suckerrr!
Swearing/bleeps
Triangles
Trouble at the Command Center
Water Skii's