Rule #1: Never let suspects stay together. (Ep 101 "Yankee White") (Confirmed as #1 in Ep 811 "Ships in the Night" although the fact there were two #1s was mentioned)
Rule #1: Never screw over your partner. (Ep 414 "Blowback") (Confirmed by McGee as #1 in Ep 917 "Need to Know")
Rule #2: Always wear gloves at a crime scene. (Ep 101 "Yankee White")
Rule #3: Don't believe what you're told. Double check. (Ep 101 "Yankee White")(Confirmed as #3 in Ep 901 "Nature of the Beast")
Rule #3: Never be unreachable. (Ep 313 "Deception")
Rule #4: The best way to keep a secret? Keep it to yourself. Second best? Tell one other person - if you must. There is no third best. (Ep 414 "Blowback")
Rule #5 You don't waste good (Ep 822 "Baltimore" and Ep 901 "Nature of the Beast")
Rule #6: Never say you're sorry (Ep 711 "Flesh and Bone" also mentioned, but without a number, in Ep 313 "Deception" also said in Ep 902 "Restless")
Rule #7: Always be specific when you lie. (Ep 123 "Reveille")
Rule #8: Never take anything for granted. (Ep 310 "Probie") Mentioned in Ep 921 "Rekindled", but as never assume? (also in Ep 1012 "Shiva")
Rule #9: Never go anywhere without a knife. (Ep 113 "One Shot, One Kill" and Ep 120 "Missing")
Rule #10: Never get personally involved in a case (Ep 721 "Obsession") (Confirmed by McGee as #10 in Ep 917 "Need to Know") "Never get involved personally on (in?) a case"
Rule #11: When the job is done, walk away. (Ep 624 "Semper Fidelis")
Rule #12: Never date a coworker. (Ep 115 "Enigma")
Rule #13- Never ever involve lawyers, things are bound to turn nasty. (Ep 607 Collateral Damage)
Rule #15: Always work as a team. (Ep 505 "Leap of Faith")
Rule #16: If someone thinks they have the upper hand, break it (Ep 824 "Pyramid")
Rule #18: It's better to seek forgiveness than ask permission. (Ep 304 "Silver War", also Ep 711 "Ignition")
Rule #22: Never, ever bother Gibbs in interrogation. (Ep 410 "Smoked", also mentioned in Ep 919 "The Good Son")
Rule #23: Never mess with a Marine's coffee if you want to live. (Ep 209 "Forced Entry")
Rule #27: (When following a suspect) There are two ways. First way they never notice you, second way is they always notice you. (Ep 715 "Jack Knife")
Rule #35: Always watch the watchers (Ep 822 "Baltimore")
Rule #36: If you feel like you're being played you probably are. (Ep 901 "Nature of the Beast")
Rule #38: Your Case, Your Lead (Ep 616 "Bounce" and Ep 10.03 "Phoenix")
Rule #40: If it seems like someone is out to get you, they are. (Ep 722 "Borderland" and Ep 724 "Rule 51")
Rule #42: Never accept an apology from someone who's just sucker punched you. (Ep 916 - "Psych Out")
Rule #44: First things first, hide the women and children (Ep 724 "Rule 51")
Rule #45- sort of- Gibbs said he would be cleaning up the mess he made and Tony leans over and whispers to Ziva "That's rule 45. Sort of (Ep 724 "Rule 51")
Rule #51: Sometimes- You're wrong (Ep 724 "Rule 51")
Rule #69: Never trust a woman who doesn't trust her man. (Ep 907 "Devil's Triangle")
Mentioned as rules, but with no number given
-'no eating in autopsy.' (Tony mentions to McGee after correcting himself that it isn't 'no eating in the truck' as he first claimed)
eta- see the comments for a vid someone put together about many of Gibbs' rules.
eta- According to Tony in "Collateral Damage" seven of Gibbs' rules involve lawyers, but #13 is the most important one.
eta- apparently all of the rules in the 40s are the serious/bad ones.
Final eta- I stopped watching NCIS early in S10 so if there have been any rules given or changed since then this list won't include them unless someone comments/messages me with them.