A.  E.T. The Extra-Terrestrial

ILM has sneaked in a trio of E.T.-Like aliens in the Senate Rotunda scene. (If any of you out there remember, this one's kind of a reversal. In Steven Spielberg's E.T., there was a kid dressed up as Yoda.) They are clearly visible for a fraction of a second, and at almost the same time as the...
 

B.  Wookies!

Yes, the Wookies are back!! George Lucas said in an interview that Chewbacca would probably not appear at all in the Prequel Trilogy, but you would see Wookies. Well, he kept his word! They appear in the Senate Rotunda scene along with the E.T.'s.
 

C.  Warwick Davis

The actor most famous for his title role in the movie "Willow" (written and executive produced by George Lucas) and the man behind the Ewok Wicket in ROTJ, makes a few remarkable appearances in TPM. The first of these characters is Wald, a young Rodian (Greedo from ANH being an adult example of a Rodian) who is friends with Anakin Skywalker in Tatooine.

Next, in the pod race scene, the human with semi-long hair talking to Watto during the race is ALSO Warwick Davis

Finally, in the last scene (the ceremony on the capital of Naboo, Theed,) you see Warwick a third time, helping a Gungan (can't remember if it's Jar Jar right now) step off the creature he was riding by holding its reins.
 

D.  Darth Vader's breathing sound

This one is NOT a rumor! At the end of Episode I credit roll, you hear Darth Vader breathing. (I definitely heard it as the credits music ended.)
 

E.  Jabba The Hutt

Jabba is noted in this section not because he clearly appears in the movie, but because he appears in the acting credits. Jabba is played by "himself."
 

F.  Battle Droid 1138 & other THX references

At the end of the battle between the Federation Battle Droids and the Gungans, the back of a deactivated droid displays the nummer 1138. That reference is definitely there, but people have made claims that the number 1138 is all over the movie. If anyone is aware of these occurences, please e-mail me at ep1faq@hotmail.com with it.
 

G.  Rumored & Uncomfirmed

Currently, there's very little in this list. I'm currently scrounging for rumors.
To date, all I've heard is rumors of Grim Fandango, a Lucas Arts game character, appearing in the Pod Race scene.

Appendix A: LINKS