Back to the original question, here's what I do:
1. Establish a city, hopefully your capital, to emphasize science through commerce. This needs to be a place with a lot of food potential (flood plains, a food special or two). Put down a farm or two in the beginning to grow the pop, then put down cottages everywhere you can if you have the people to work them. Build library and university, eventually observatory and Oxford there.
2. It helps if you're a financial civ, and if so try to put your cottages by a river, for instant +3 commerce.
3. Gold, silver, gems and dye also produce nice commerce.
4. If your capital is your science city, go into bureaurcracy as soon as you can.
5. This probably won't work if you're a spiritual civ, as you may have a religion or two founded in your capital, and you'll want this to be your money city. Select another city to be your science city.
6. Everywhere other than your science city (and other special purpose cities such as military/production cities or relgion/money cities), put down a bunch of farms. Build libraries and maybe universities, and hire science specialists in those other cities.
7. Don't grow too fast. If you find you're having to move the slider down to 60 percent science or less, stop and consolidate and improve your current cities.