This is a living page and will be updated periodically as the firmware is changed and my experience with it grows. At the time of writing, the current version of Repetier Firmware was 1.0.3.
The settings in the firmware are divided into two categories: hard-coded firmware settings and EEPROM settings. The EEPROM settings are visible in the Firmware setup, but will be ignored since the EEPROM will be activated.
In general, leave the settings as default unless they are addressed below.
Configuration level: set to Expert - show everything
EEPROM usage: EEPROM Set 1
Allow quad stepping: Enable if using an 8-Bit AVR controller (ie. RAMPS)
Delay stepper high signal: 2 (allows use of DRV8825 drivers)
Delay stepper direction signal: 4
Delay between double / quad steps: 2
Move Cache Size: 32 for Cartesian printers, 16 for Delta printers
Ensure minimum time per move when cache is below: I set to 2/3 of Move Cache Size
Review any warnings on this page. In particular, I tend to forget to activate the watchdog timer. These warnings are usually important!
The extruder speed is set by the Max Speed, Start Speed, and Acceleration parameters. Max Speed and Acceleration are, well, the maximum feedrate and feedrate acceleration of the extruder motor (1). The Start Speed is the 'Jerk(2)' of the extruder.
In my experience, setting the Start Speed too low can cause significant motor skipping. At this point, I would simply recommend that the Start Speed is somewhat lower than the Max Speed - maybe 1/4?
In general, the extruder is only going to reach these limits during retracts or non-printing operations (such as changing filament). As such, set these parameters with very short extrusions (Less than 2mm for direct-extruders, Less than 10mm for bowden extruders) in mind.
(1) The extruder feedrate is also limited by the max step frequency and step combining (is double-stepping allowed?).
(2) Jerk, as defined by most open-source 3D printer firmwares, is the starting speed of a motor with no prior ramp-up acceleration.