I wouldn't say there are good or bad proteins or amino acids.
Just some basic info though:
Proteins from animal sources are "complete." That is, they contain all the essential amino acids. Proteins from vegetable sources (or grains) are "incomplete." They either do not contain all the essential amino acids, or are so low in some of them as to be considered incomplete. You can get all your essential amino acids from vegetable sources alone, but you do have to be careful about eating a wide variety to make sure you're getting 'em all. (Hence the rice and beans combo in some Central American countries, or even succotash in the South - beans and corn.
Some amino acids convert more readily into glucose than others. Alanine, for example, is considered the "most gluconeogenic amino acid." Bear in mind this is not a bad thing, even if you're trying to lean out or control your blood sugar. I see no reason to worry about limiting alanine intake. (That would be pretty damn difficult to do anyway.) I'm a huge low-carb fan, but even I understand we'd be in big trouble physiologically if gluconeogenesis ever failed us.
A few amino acids have specific roles that can be helpful specifically for certain physical and/or psychological issues. Glutamine is excellent for helping repair the gut (or any cells with a rapid turnover, actually, but it's especially recognized as being good for gut healing). Phenylalanine, tyrosine, and tryptophan are precursors to certain hormones and neurotransmitters (serotonin, dopamine, thyroid hormone, epinephrine, etc), and some people have experienced great benefits from supplementation with them for specific conditions like depression, anxiety, eating disorders, mood issues, etc. This isn't to say you should look for foods that are high in these...some of them compete with each other for entry into cells. Depending on someone's needs, some would be more important than others, and it's important to know the intake directions (on an empty stomach vs with food, by itself or in combination with other amino acids or vitamins, etc.)
Overall, I think the simplest advice is the best where protein is concerned: make sure you're getting enough total protein, preferably from animal sources, and if you have a specific condition you'd like to improve, look into supplementation with individual AAs. (And if you're looking to add muscle mass, eat MORE protein!)
Glutamine is a good AA -- it's the preferred food of the cells which line the GI tract, and is the most abundant amino acid in muscle tissue. Together with cysteine it's the building block of glutathione, a super critical antioxidant. Glutamine also acts a neurotransmitter (via glutamate) and can be very calming for ADD types.
If you are prone to cold sores (Herpes), lysine is your friend, and arginine should be avoided.
Nutritionists used to refer to animal proteins as "first class" and plant proteins as "second class" based upon digestibility and completeness of the essential amino acid profile. Then vegans got offended. That's about as far as I care to worry about good or bad proteins, particularly given the bonus stuff that first and second class proteins are naturally packaged with.
Best is animals that eat grass like beef, bison, and lamb or wild caught fatty fish. Next best would be animals that eat some grains like pastured pork or chicken. Last would be factory farmed meat or fish. Check out the Bulletproof Exec One Page Bulletproof Diet.