OH loook ! This was my #1000 post !! Ok, that's official, I'm a crazy nuts. 
1000 Posts!Oh, I'll be wearing out Checkmate & probably Veiled Threat too. 
B
I totally agree, Duffy. I think the acting in Checkmate was superb, and it's one of my favorite episodes.
I believe the circumstances in the scenes you are noting are really different cases. Peter didn't do anything dishonest that endangered Kate's life, and in everything he did (like withholding information from Neal) he was trying to protect Neal... he might not have always been right in the way he did it, but I believe he always intended to protect Neal's emotional and physical health, and Neal's future, as much as he could. I think Neal's (and Mozzie's) dishonesty with the treasure indirectly endangered Elizabeth's life... none of what they did was intended to protect Peter (or anyone else). As for Jones, I took it that he acted unprofessionally and lacked self-control on the job. Peter and Neal may lose their temper with each other, but they always keep their emotions in check when dealing with criminals (except for maybe Keller!)
Checkmate is my favorite S3 episode. The acting was phenomenal; right up there with Countdown!
I loved Peter in Where Theres A Will. He was so excited to go on a treasure hunt. Yeah, Tim Dekay's facial expressions are great.
As for the shirtless scene, like I said before, if they are on an island that can lead to shirtless scenes.