Neo’s apartment: 101
Heart o’ The City room: 303

Neo is not currently The One as he’s running to get to this room.  Neo, being an allegorical character to the second part of the Trinity, could be why the middle number is a zero.  Because here is where he would meet his death.  Also, representatives from the machine city of Zero-One were inside of the room.

Crew’s license tag: AA 034 (AA, popular type of battery)
Agents’ license tag: 70858
Date on computer in opening: 2-19-98 13:24:18
Date/time on computer in closing: 9-18-99 14:32:21
Time on Neo’s clock when he is awoken by the alarm (after having met Trinity for the first time): 9:18
Phone number traced in opening: 555-0690
Plate on the Neb: MARK III No. 11 / Nebuchadnezzar / Made in the USA / Year 2069
Mark III No. 11 could refer to Bible verse Mark 3:11 – “And whenever unclean spirits saw him they would fall down before him and shout, “You are the Son of God.”
On the 3 blocks at the Oracle’s: 3,9,V,Z,P,L,I,W
Phone number for City Boarding, printed on the walls of room 303: 555-0156
Phone number on Guns billboard: 555-0161
The building they land on top of after swinging from the helicopter is the “mmi” building. In Roman numerals, mmi = 2001.
The Oracle’s apartment number: C960 (9th floor.)