I play an Oracle, and search for two cards. While I am searching, I find that I have a HUGE energy pocket coming up. So I break it up and add some trainers in between them. I then shuffle and put 2 cards on top. Is that legal?
As long as you shuffle sufficiently afterward.
Source: PUI Rules Team (2004-03-25)
I was playing with this guy and he rearranged the order of the cards in his deck prior to shuffle it, would this be allowed in a tournament?
Yes but you would have the right to shuffle it yourself or cut it as well if you were uncomfortable with his shuffling method.
Source: WotC Chat (2000-09-15)
Is it illegal to randomly shuffle your deck, and if yes what are the penalties from doing so?
Yes it is illegal. The penalties depend on the tournament rules.
Source: WotC Chat (2000-08-31)
At any time during a battle, are you or your opponent allowed to shuffle your deck?
NO! [Ed. Note: This references shuffling at random times, not when appropriate]
Source: WotC Chat (2000-06-29)