Miscellaneous Symbols and References in the Trilogy:

"Loop"

* "Loop" is written on the subway train in The Matrix and Revolutions
Maybe this has something to do with the constant rebooting of the Matrix.

"Heart o' the city Hotel"

* The hotel where Trinity fights the police men and where Neo is shot by Agent Smith The Matrix

Names of buildings, companies and streets

* DISCO SYSTEMS (when Neo "does his Superman thing")
This could be a possible reference to Cisco Systems?
* EON (when Neo "does his Superman thing")
'Eon' is an anagram of Neo
* ESC (when Neo "does his Superman thing")
Escape?
ESC entertainment is mentioned as a special effects company for the Matrix movies: http://us.imdb.com/title/tt0234215/companycredits

Mobil Ave

* 'Mobil' is an anagram of Limbo

Ships - Captains

Brahma - Kali
Logos - Niobie
Osiris - Thadeus
Gnosis - Ice
Vigilant - Soren
Hammer (Mjoinir) - Roland
Caduceus - Ballard [Bane is on the Caduceus]
Icarus - Ajax
Nebuchadnezzar - Morpheus
Novalis - Tirant

Thanks in large part to: http://matrix-explained.com/symbolism_in_the_matrix.htm