There are many great guides for tuning and calibrating your printer out there, but there are a few techniques I heavily employ that don't seem to get much discussion.
After you've squared your axes, made everything that should be rigid, extremely rigid, tightened your belts, tuned your heatblocks, and calibrated your extruder steps/mm you might think the tinkering ends there.
The truth is that the slicer settings play as large of a role in the quality of your prints as does your mechanical setup. This is probably obvious to many, but there are some less than obvious adjustments you can make in the software to improve your print quality.
One of the most important considerations that I don't see frequently discussed is choosing an appropriate nozzle size/layer width combination for each individual print. Every single print is designed somewhat differently regarding the width of walls and other design features.
You want to choose a nozzle size and layer width combination that perfectly matches your wall thicknesses. I keep a variety of nozzles on hand from 0.3mm to 1.2mm which gives me an effective range of 0.33mm to 1.5mm layer widths. You almost always want to set your layer width to be larger (ideally 120%) than your nozzle diameter. The process is slice your model, inspect thin walls, if there aren't enough perimeters, reduce your layer width until your thin walls are filled with perimeters. Do not reduce layer width below 95% of your nozzle diameter or your print quality will begin to diminish.
At Telemetry3D we have three printers; by default they are setup as follows:
E3Dv6; 0.3mm Nozzle (0.33mm layer widths, 3 perimeters) - Slow high resolution printing
E3Dv6 Volcano; 0.4mm Nozzle (0.5mm layer widths, 2 perimeters) - Balanced, standard resolution printing
E3Dv6 Volcano; 0.6mm Nozzle (0.75mm layer widths, 1-2 perimeters) - Fast, strong parts, high resolution vases, economical resolutions.
Once you've determined the appropriate nozzle size and layer width combo for your print (as well as your layer height), its on to printing.
For every new part we print I always watch the first 10 layers or so and make adjustments to the extrusion multiplier on the fly. By watching the first few layers you can determine if you are over/under extruding by simply watching where there is 100% infill. Turn up or down your extrusion multiplier until the infill layers overlap but do not bubble up. Then watch your perimeters carefully and if the perimeters look rough simply reduce the extrusion multiplier 2% per layer until your layers look nice. Be careful, under-extrusion results in extremely fragile parts.
Don't forget to write down your settings so next time you can slice it up correctly from the get-go.
Another point I want to stress is print speed.
Slow your prints down. I don't know how many sub-par prints I've had to throw out because I didn't want to wait an extra 4 hours for it to print. 40-60mm/s is plenty fast and if you need to go faster you can either spend a lot of money on an expensive machine or for the same cost purchase several additional slow machines. Either way you will be happier with your prints if you are more patient with them. Sometimes I forget that we are translating the digital into physical, once the object is created it exists and you have to look at it or work with it every day. It is no longer a file on a computer that can be hidden in a folder, if it looks like crap you end up just throwing it out, and what a waste.
Layer Height Resolution:
For high speed prototyping where turn around is most important, 250-300microns is a great high speed resolution that still looks great.
For most parts 150microns will produce the best balance between aesthetic results and print time.
For extremely detailed parts 100microns is about the limit of diminishing returns on most FDM printers. While we can print down into the 10micron range the limitations of plastic extrusion technology take over. Prints made at 25microns do not look much better than prints at 100microns, yet they take 4 times longer.