I primarily use roughly (since we're going metric, here) 3mm diameter, 1.5mm thick disks, although I did pick up a few 6mmx2mm disks for larger parts. I've found that most parts that are heavy enough to require more pull strength are also large enough to accommodate multiple magnets, so much larger sizes are rarely needed. High-torque joints are generally better served by a pin to support the part, with a small magnet keeping it from rotating and/or popping off.
I prefer disks to squares, as they're easy to fit flush and I want my joints as seamless as possible - just drill a shallow hole with the appropriately sized bit, dry-fitting to check depth, add a dab of
CA glue, and shove it in Some folks like to use a tiny blob of epoxy putty to completely fill the hole, but I've found a tight fit and a dab of glue to be more than sufficient. They're actually a royal pain to remove if you botch the job, so dry-fit like crazy to avoid alignment errors.
I keep the magnets in a stack to maintain proper polarity and make handling easier. The stack acts as a handle, which you can slide away once your glue has set. Since all magnets in the stack will also be oriented in the same direction, I can use a few "spacer" magnets when installing the second one, reattaching the stack to the first part and simply shoving the accompanying piece onto the opposite end of the stack, guaranteeing proper polarity.
Here's a Dakka article on vehicle magnetization, which covers a few different projects with some general advice. Really, though, it just takes a bit of thought. I magnetized my Predator completely differently, because I had different priorities - all of my magnets are small and countersunk to maintain the model's aesthetic. I also wanted to keep all parts' full range of motion, so I replaced the pins and sockets on the weapons with small magnets, allowing them to pivot like the stock model. It's more fiddly this way, but with a bit of planning, was doable by the novice I was, at the time.