1. First, let me say that I know of no way to specifically activate these bugs. They just happen, very rarely. I myself have only seen the bubble egg twice and the fly egg once.
2. The Bubble: Very rarely, if you blow your horn, a large bubble will rise out of it and float to the top of the screen.
3. The Fly: Go to the Cobbler's section of town and, extremely rarely, a large fly may buzz around in the center of the screen. Looking at it will yield the message "Oh no! There's a bug in the program!"
4. The Pig: At the end of the game, when you're infiltrating the monastery to save the knight, play until the Will-O'the Wisps have guided you to the tower. Instead of climbing the tower, row the boat one screen left. You will come upon a gate, a monk will spot you, and normally a rock will be thrown down and kill you. Rarely, however, a squealing pig will be thrown down instead (you still die though).
5. Again, I know of no way to activate these, so I suggest saving your game just before doing the actions so that if it doesn't happen you can reload, and so on and so on. If you find a way to activate these, please e-mail me.
6. Enjoy!