Also this program is 3x5, not 5x5. I have noticed my last 2 sets on 5x5 are much weaker than the first 3.

It's still a 5x5, just with 3 working sets.
The 5x5 programs with 5 working sets are volume programs. Better for size increase.

The point of both is that when you can complete all working repetitions you add 5-10lbs. to the movement on the next session.

Good article! for a good while an old training partner would go to the trouble of bringing his own smaller then standard size weight plates to the gym.

For years I carried 0.5lb. & 1.0lb. fishing weights with wire loops attached to put them on the end of the bars.

No matter what your body comp goal is the road to accomplishment is paved first and foremost with the NEED to add MORE muscle! Especially for women!
 http://www.t-nation.com/free_online_article/most_recent/who_wants_to_be_a_novice_you_do

I've been noticing this thread for a while, but I just have one question puzzling my mind:
What does the article mean by warm-up set?
How do you do warm-up sets?

And how should I avoid joint injuries..as before I tried doing squats and my knee was making some weird sound

The guy in the link suggests one of the 7 exercises to be chins. What if you're a chick and either don't have the ability or equipment to do chins.

What's an alternative to chins?

Hopfully you have a Squat rack, Smith or some other bar
http://www.youtube.com/watch?v=vM-b4qOOWsE

Source?

"Rapid Lean Body Mass Growth is Always Accompanied by a Bodyfat Increase.

Always."

Any comments on this - from a paleo point of view?

I think the key word there is "rapid".