These are some common things/subjects that I feel come up, or things that I've experienced and wanted to share.
Printer won't connect to Simplify3D
1) Check Baud Rate to be sure. Generally 115200, or 250000 for most printers. Some printers use other Baud Rates, this information should come with your printer.
2) Ensure USB drivers are installed (If Simplify3D doesn't show your USB port for your printer, chances are there's no driver so your computers not able to recognize the USB detection. Key test, can you connect to the printer using a different software program?
RepRap style Arduino/Ramps board: install Arduino IDE that will install the proper drivers (Mendels, Prusa's, RoBo 3D, anything with an Arduino Mega on it)
LeapFrog 3D printers: FTDI drivers http://www.lpfrg.com/support/installation
Ultimaker FTDI drivers: http://wiki.ultimaker.com/FTDI_Driver_installation
Rambo Board- http://reprap.org/wiki/Rambo#USB_Driver (SeeMeCNC Orion/Delta MAX, Lulzbot Taz, Airwolf printers, MakerGear, new Mendels)
MakerBot/Sailfish- I would recommend installing ReplicatorG as that will include drivers as needed
MakerBot 5th Generation- Windows 7 and 8 may already have the necessary drivers, but if they don't installing MakerBot Desktop should fix this.
3) (If MakerBot/Sailfish style machine) Open MakerBot Desktop, go to Services and select Stop Background Services. Background Services will connect to the printer even if MakerBot Desktop isn't open, so if you try to connect with Simplify3D, Simplify3D will get an error since the printer's already connected to another piece of software!
Printing over USB, Firmware Unresponsive error in machine control panel/print stops randomly
There are a few reasons this could be happening. However, I personally avoid USB printing at all costs as I find that the added risks of a failed print from USB cable transmission/PC issues is not worth it.
CNC machines are extremely similar to 3D printers and even run off of G-Code, however if you were to use a USB cable to stream G-Code to your CNC machine, that would be ridiculed as terrible design. The CNC machines I've worked with use either a flash drive or SD card for data transmission. With 3D printing, the stakes are a lot lower, if you lose a print due to streaming USB transmission failure from your PC, it's potentially only a few dollars in plastic and few hours wasted. With CNC machines, it could be a block of titanium worth 1,000 dollars being cut, so the CNC designers definitely would not have the added risks and add chance of failure in transmission.
Reasons why computer to USB transmission should be a secondary choice to SD card printing:
Main reason-->USB cables are prone to EM interference- If too many transmissions get dropped in the back-and-forth the firmware will go unresponsive.
Computer's sleep settings may be on
Laptop could run out of battery
Automatic system updates restarting the computer
If your processor lags (playing a video game that requires high performance)- transmission could be interrupted
Accidentally closing the software
Computer freezing due to another program
However, if you're crashing still over SD card, one possibility is that your microprocessor is overheating. I've had this on a Ramps Board occur, which was remedied by adding a small fan to the power supply rails.
Upgraded to new version of the software, new profiles aren't showing up
Installing the new version, doesn't uninstall the old version, so it can be an easy mix up to accidentally open a previous version if the shortcut on your desktop is linked to the old version or if your file association your computer is associated with the old version.
However, if you are opening the new version of the software, this can be fixed by going to Help-->Reset All Settings
(RepRap/Marlin style printers)Added an extruder to my printer, toolhead offsets are off
The firmware controls the toolhead offsets, however you can also adjust the value at the start of each print under the Scripts tab. There's the Starting G-Code where you can add tool head offset G-Code commands. For instance, if there's a 33 mm offset in the X direction between your right and left extruder, place these two commands at the beginning of your starting G-Code.
M218 T0 X0 Y0;
M218 T1 X33 Y0;
(MakerBot/Sailfish) Left Extruder/Heated Bed is not working. Or print is not to size
http://forum.simplify3d.com/viewtopic.php?f=8&t=1944
RepRap Prints are not to size
http://forum.simplify3d.com/viewtopic.php?f=8&t=1937