It's great you are reaching out. Three can be a tough age, and it sounds like your little one is pushing the limits. Not listening, screaming when he does not get his way, or running off without supervision can not only become a habit for him and a headache for you, but a big safety concern. Kids his age can be very headstrong because they are at that developmental age in which they realize they are independent little beings. They can do so many more tasks on their own like get that toy down from the shelf or run to a pet or friend in another yard, yet they still need supervision, instruction, and sometimes re-direction.
They still are at that stage in which they don't want to be interrupted during play or a TV show when it's time for dinner, the bathroom, or time to simply follow a direction from a parent, because they don't want to miss out on something. They are only just beginning to realize they might be able to come back to this activity. Perhaps times like these are when you are finding that he is either ignoring you or failing to follow a direction from you and instead begins to whine.
Behavioral charts, time outs, and talking it out are all good strategies, but if they are not working, you might want to start at the beginning and “re-train" your son by pre-teaching and practicing expectations often during neutral times. This will take just a minute, but do a role play 3-4 times a day.
“When Mommy asks you to do something….."
STOP
LOOK
OK
DO
Start with little things like have him pick up one toy or hold your hand right there in the kitchen. You can even make it fun by having him make a funny face or eat two animal crackers. Praise him with a kind word, a hug, or a short story and be sure to review right away. “You stopped, looked, said OK, and held my hand, now we can have time to read a book." If he did not follow your instruction, you re-teach again. All of this helps him learn a social skill -- how to follow an instruction.
Be very matter of fact throughout these exercises. There is no need to raise your voice even if he is screaming. It is a win for him if he draws you into the screaming match, and he will do it again and again with the hope you will scream again. We do not know what his timeouts looked like, but start again by sitting there with him (activity free) until he is calm and then his 3-minute timeout can begin. If this means sitting in a room with no toys, go to that room, leave the door open, and just sit at the entrance. If you are out in public, you can go to your car or another aisle (somewhere away from where he wanted to be). All of this is going to take extra time for you, but be consistent and give this a month to see if his screaming decreases and his following an instruction increases.
You can even set up some false outings to give him more practice. The outing can be something little like a park or a friend's home, or even a grocery store. Wherever it is, it must be a place he LIKES to go to and is meaningful to him. The minute he does not follow your instruction, you leave. The re-teaching cannot begin until he settles down again, but these false outings are great ways to practice.
Look at boystownpress.org, too. There is a great book called Common Sense Parenting that you might like. It covers all kinds of social skills for the toddler and into elementary school age, such as how to accept “no" for an answer or how to wait your turn. Every six months you will need to re-evaluate what is meaningful to him, too. Last year it might have been a special blanket, but this year it could be his Transformer action figure.
Please do call anytime if you need a listening ear. You are not alone. Parenting is a hard job, but any of the crisis counselors here would be more than happy to talk to you.