Agenda Rulings

AI Chief Financial Officer
Though the card text is not specific, you shuffle into R&D all of the cards stored in HQ and the Archives. (Official Netrunner Rulings, 4/21/97)

Artificial Security Directors
If the difficulty of an agenda is reduced to zero or less, it must still be installed to be scored. (Sparky, Netrunner-L, 5/19/96) 
Scoring multiple Artificial Security Directors produces a cumulative effect (i.e., scoring two will reduce the difficulty of Black Ops agendas by 2). (Sparky on Executive Extraction, Netrunner-L, 6/25/96)

 Corporate Headhunters
Note that while the first ability mimics brain damage, it is not actually brain damage, so ignores effects that would prevent, remove, or otherwise interact with brain damage. (Official Netrunner Rulings, 4/21/97)

 Data Fort Reclamation
You may use additional bits from your bit pool to rez and install the cards. (Sparky, Netrunner-L, 10/18/96) 
Note that you are not gaining actions in order to construct the data fort, but simply constructing it as a result of scoring Data Fort Reclamation. So this card does not supply actions you can forgo in order to get rid of virus counters, for example. (Official Netrunner Rulings, 4/21/97)

 Employee Empowerment
The additional draw provided by Employee Empowerment is a start-of-turn effect separate from the normal draw; the Corp can draw one card and look at it before deciding whether or not to draw another card. (JD Wiker, Netrunner-L, 1/28/97)

 Executive Extraction
See notes on Artificial Security Directors.

  Fetal AI
The Runner may choose not to pay the 2 bits and not steal Fetal AI; Fetal AI is still considered to be accessed. (Sparky, Netrunner-L, 10/2/96

 Genetics-Visionary Acquisition
See notes on Artificial Security Directors.

 Ice Transmutation
If the Corporation scores Ice Transmutation and uses it on a piece of ice that is subsequently derezzed but not removed from play, the ice remembers that it was affected by Ice Transmutation. If that same card is uninstalled or trashed and later replayed, it does not remember the change. (Netrunner FAQ v.1.0, 5/22/96) 
This effect doubles all subroutines provided by the ice itself, even those that are generated after Ice Transmutation takes effect. It will not double subroutines provided by other abilities; for example, two Ice Transmutations don't double he subroutines the other Transmutation provides. However, it will double subroutines that are not actually printed on the card; for instance, Ice Transmutation will repeat the subroutines generated by the card text on Minotaur (note that this is a reversal of a previous ruling). (Official Netrunner Rulings, 4/21/97)

 Marine Arcology
In order to get the benefit of Marine Arcology, you must have two actions immediately available to you; actions must be consecutive and they must all be spent on the same turn. (Sparky on South African Mining Corp, Netrunner-L, 5/16/96)

 Please Don't Choke Anyone
When any effect owned by the Corp does preventable damage, Please Don't Choke Anyone can prevent that damage to gain a PDCA counter (e.g., the Corp could prevent the damage done by a Mastiff counter to gain a PDCA counter). (Tom Wylie, 8/26/97)
The Runner has the opportunity to prevent damage before the Corp can use Please Don't Choke Anyone to prevent that damage to gain a PDCA counter. If the Runner prevents it, then it is not successful and no counter is given. (Skipper Pickle, Netrunner-L, 8/26/98)

 Priority Requisition
"At no cost" does not cover additional "above the rez cost" costs (cf. Caryatid or Digiconda), since these are not part of the rez cost. (Sparky, Netrunner-L, 9/5/96) "At no cost" means you waive the normal bit/action cost for whatever the action is, as well as any special costs listed in the text; all outside penalties still apply. (Tom Wylie via Sparky, Netrunner-L, 9/6/96)

 Project Babylon
The Runner only scores 1 agenda point for stealing Project Babylon, regardless of the number of advancement counters on it. (Sparky, Netrunner-L, 5/22/96)

 Security Net Optimization
The fort gives the bonus to ice installed on it before and after Security Net Optimization is scored. (Sparky, Netrunner-L, 6/18/96)

Security Purge
"At no cost" does not cover additional "above the rez cost" costs (cf. Caryatid or Digiconda), since these are not part of the rez cost. (Sparky, Netrunner-L, 9/5/96) "At no cost" means you waive the normal bit/action cost for whatever the action is, as well as any special costs listed in the text. All outside penalties still apply, so the Purge still has to account for Restrictive Net Zoning and similar cards. (Tom Wylie via Sparky, Netrunner-L, 9/6/96) 
If the Corp scores Security Purge when there are fewer than three cards left in R&D, the Corp shows as many cards as there are in R&D to the Runner and fulfills as much of the Purge effects as possible; since the effects do not require the Corp to "draw" the cards, the Corp player cannot lose the game by scoring this agenda. (Skipper Pickle, Netrunner-L, 7/17/98)
Security Purge says ‘rez them, at no cost’. ‘No cost’ refers to the number in the upper right corner of a card. Security Purge doesn’t let you get out of paying Glacier’s agenda point cost. Reverses ruling above.
Note that Security Purge instructs you to install and rez the ice, which means you have to do so if possible. If there are additional costs to install + rez, and you can pay them, you have to install + rez and pay those costs. I.e, if you’ve scored any agenda, and Security Purge turns up Glacier, you have to install + rez Glacier, and therefore spend 1 of your agenda points.(Tom Wylie 11/12/99)

 Subsidiary Branch
Barring interaction from other cards, the Corporation will have four actions per turn for the remainder of the game, including during the turn in which Subsidiary Branch is scored. (Netrunner FAQ v.1.0, 5/22/96)

Theorem Proof
If the Runner chooses to install Theorem Proof as a program it is not considered stolen. So you can't play Trojan Horse afterwards.
Bizzare Encryption Scheme can not prevent the Runner from installing Theorem Proof as a program. But if the Runner does not install it and it is still in the fort at the start of the next Runner turn the Runner scores Theorem Proof without having to install it.

Viral Breeding Ground
If Viral Breeding Ground returns a daemon to the Runner's hand, the programs installed inside it are trashed; there is currently no effect in the game that will prevent the trashing of these programs. (Sparky, Netrunner-L, 9/5/96) 
Any advancement counters on Viral Breeding Ground are not considered Virus counters; they're just advancement counters that happen to be on a Virus card. (Sparky, Netrunner-L, 10/2/96)

 World Domination
The Runner only scores 3 agenda points for stealing World Domination, regardless of the number of advancement counters on it. (Sparky on Project Babylon, Netrunner-L, 5/22/96)