Meanings of numbers in the Matrix:

101

* Neo's apartment in The Matrix
* The Merovingian's floor level (when Neo visits him in his restaurant)
* The highway chase in Reloaded is on Highway 101.
* It is sprayed on the wall when Neo talks to the Oracle in Reloaded.
* "Room 101" is a torture chamber (George Orwell's 1984)

303

* The room where The Matrix starts, with Trinity fighting the policemen
* The room, which is the very same room as above, where Neo is shot by Agent Smith in The Matrix.

16 females, 7 males

Architect: "The function of the One is now to return to the Source...After which, you will be required to select from the Matrix 23 individuals - 16 female, 7 male - to rebuild Zion."

* 23 is half the number of human chromosomes (46)
* Genesis 7:16 (NIV): “The animals going in were male and female of every living thing, as God had commanded Noah. Then the LORD shut him in.”

Pi (=3.14...)

* Smith, when possessing Bane, cuts a Pi symbol into his hand
* Neo has 314 seconds to enter the door to the Architect

#6

* Neo is the 6th integral anomaly
* On the 6th day, man was created and all god's creations completed. On the 7th day the god of the bible takes a rest
* The TV series The Prisoner features the hero which is held captive and given the number #6. As Neo runs through the old lady's apartment who throws a knife at him near the end in The Matrix, we see an image on the TV of a menacing man in a black suit coat. The image is that of #2 from this TV series.
* 6 is mathematically the first perfect number (= a number that is the sum of its divisors): 1+2+3=6
* The are 6 anagrams of "n-e-o":

"Mark III No 11 Made in the USA Year 2069"

* "Mark 3 #11 M" is Morpheus' ship's number.
* Bible: Markus 3:11
"Whenever the evil spirits saw him, they fell down before him and cried out, 'You are the Son of God'."
Bible: Markus 3:12
"But he gave them strict orders not to tell who he was."

12 o'clock

* Trinity goes to the power station at 12 midnight.
* Neo goes to the Merovingian's restaurant La Vrai at 12 noon.

18th September

* At the end of The Matrix, Neo is seen in a phone booth. The datum shows "9-18-99". September 18th is the birthday of Andy Wachowski's wife Alisa Blasingame.

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