Do everything in the most logical order.
Clean your bench before you begin working. Set a space aside for parts you're working with, so you won't lose them. Especially important when working with small screws and bearings.
Make sure the wheels are both straight in the dropouts and true before you adjust the brakes. Otherwise, you may waste your time tuning the brakes initially, because you'll have to reset and/or true the rim and then adjust the brakes again afterwards. This also applies when using the Park Tool DAG-1; if the rear wheel is crooked, so will be the derailleur hanger if you use the wheel as reference.
Make sure any part you're working with is in good condition before reinstalling it. If it's likely to cause problems, fix or replace the part now.
If a bike is giving you a really hard time, relax, kick back, have a beer, and try to think of a creative solution. Preferably more creative than just using brute force
Subtract the beer if you're working at a shop, and have it after work instead. One example of changing the order of things depending on the particular circumstances.
Never, ever half-ass anything. If you do, it will come back to haunt you. Spend that little bit of extra time doing it right the first and only time, and you won't have to worry about it later. In the long run, this approach will save you time and headaches, and will also keep customers very happy. The only customer I've had come back with a problem with a bike I had worked on (aside from those who've broken or worn something of their own accord) was one with a disconnected front V-brake... I had disconnected the brake in order to remove the front wheel for transportation in her car. I assumed that she knew how to re-attach it
Now I make sure customers know before seeing them off. Live and learn.