The downtown area of Queretaro has to be the highlight of Queretaro; it is very pretty and it's the most colonial part of Queretaro. Here you can do some shopping for Mexican candy, T-shirts, Mexican art, or other small things they sell on the streets.
Queretaro is considered the cleanest city in all of Mexico and the locals take it very seriously; you'll see garbage cans every 10 steps and you won't ever see garbage on the streets.
In the main garden, there are a lot of small restaurants with tables outside so you can enjoy your meal while you admire the view. The restaurant I would recommend in the main garden is 1810.
You can also take day trips to San Miguel de Allende, Guanajuato, Peña de Bernal, or Real de Catorce.
WARNING: I live in Mexico City and I'm used to dealing with traffic and crazy drivers, but I've never ever seen such crazy drivers like in Queretaro, so be careful because they really are nuts!!!