Just finished season 2. It starts with a great episode, The Human Factor. Followed by another good episode The Eraser with Jimmy Kendell that we see later on season 3 Back From The Dead. They introduce Jack Dalton in Jack Of Lies, we also see him in Dalton, Jack Of Spies, Partners and Friends. I do like Jack Dalton as a character, but these episodes aren't my favorites from second season, except Partners where we'll get our very first Murdoc episode. Definitely one of the best episodes of this season. By the way we see lots Pete Thornton in the field with MacGyver this season.
Phoenix Under Siege what a superb episode and I think this one is my favorite. Few others that I really liked were Pirates, Marta DuBois as Barbara, OMG she was hot

. One another great episode was Out In The Cold which is one of the funniest episodes. Mac taking care of Pete in his apartment

. We also got our first flashback episode out of 3 in the whole serie. It's not really my cup of tea, but definitely better than in most of other shows. In some shows you wanna just skip them, but never in MacGyver.
So 5 of my favorite episodes were The Human Factor, Partners, Phoenix Under Siege, Out In The Cold and Pirates. Least favorites were The Wish Child, Silent World and Friends. Once again a great season and really hard to say which is better the first or the second.
Harry Jackson: There was a time when I could run all day without breaking a sweat. I tell ya: it's hell getting old.
MacGyver: Age is only in the mind, Harry.
Harry Jackson: Well, my mind tells me I'm gettin' old.