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http://www.pokerstars.com/prohibited_programs.html

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The real meat is in the Terms of Service. Unfortunately, these are ambiguous at best (and IMHO, purposely ambiguous to give them maximum range of legal enforcement).

Quoting from ToS 3.4:
"PokerStars defines an "Unfair Advantage" as a User accessing or compiling information on other players beyond that which the User has personally observed through the User's own game play."

If this clause were interpreted literally, then one could conceiveably use a "legal" program like PT for an "illegal" purpose (e.g., clocking another game that you aren't playing in).

If that information were to be used at a later point in time for some advantage, then who is going to know? How could something like that ever be fairly and reasonably enforced?

IOW, in the FAQ, they explicitly define "legal" and "illegal" software apps. However, in the ToS, it is only implied but not explicitly stated that you could be subject to punishment if you use "legal" software for "illegal" purposes.

While I personally wouldn't cheat or collude due to personal ethics, I would want to use everything available at my disposal for information gathering and analysis.

This is the modern age. Everything is done quicker and more efficiently. In a B&M ring game, I get 30 hands per hour. Online I get 60-75. In B&M, I can gather information from my surroundings and take notes for later use. Online, I take electronic notes for later use.

Personally, I don't see the ethical conflict. In a B&M, most players will not take notes while they are in the can on a break. I wll and do. So they probably lose a bit of an edge over time. Online I take electronic notes. Anyone that doesn't is probably losing a bit of an edge over time.