Well, it all depends on your age.
I can tell you what to expect 35-40ish. The doc will most likely order someone to take some blood to measure your cholesterol, triglycerides, liver enzymes, etc. He'll test your reflexes. Most likely he'll test your testicles for bumps, etc. He might give you the jelly finger to check your prostate for the first time. He'll weigh you. They'll take your temperature and blood pressure. He'll look down your throat and at your tongue. He'll feel for your lymphnodes. He'll look at your eyes. He'll look in your ears. He'll listen to your chest. He'll palpate your abdomen. He'll ask about diet and exercise. He'll ask you about your alcohol/drug use and whether or not you use tobacco. He'll do a vision test. He might do a hearing test. You might have to provide a urine sample. He'll ask about your medical history and any medications you've taken or are taking.
There should be a time for you to ask all of your questions. Oh yeah, don't forget to write down any questions or concerns before you go into the doctor so that you don't forget to ask for anything you want checked or answered. There should be a time for him to give you preliminary findings.
Oh, and go early. He'll want you to fill out scads of forms to start your chart, privacy statements, medical history, releases of medical information from previous doctors, etc. And he'll want you to bring your insurance card and your copay, or he'll want you to provide proof of ability to pay for services.
After you will most likely have to go somewhere else to get your blood drawn and it will take a week or so for the results to get back to your doctor. You'll most likely have to call the doctor to find out the results because usually they'll be normal so they won't call you to tell you. Usually they only call you if it's bad news.
Most likely he'll be very thorough because you haven't been to see anyone for so long. Then every check-up, if you do them regularly (yearly usually), they'll take less time.