Connecting multiple SPI devices to Texas Instruments CC3200 LaunchPad

I'll assume that the total length of each of your buses is under 1 meter, which is typical for plain I²C and SPI. Also, the bus capacitance is within the spec.

There should be only one (1) set of pull-up resistors. As a result, the best place for them is on the main controller board. Don't put the pull-ups on the modules.

If you want to have pull-up in some cases and not have them in other cases.

• Do not populate the pull-up resistors, when you don't need them.
• Design the main controller board such that pull-ups are connected to the signal lines through jumpers. Remove the shorting blocks, when you don't need the pull-ups.

edit: Frankly, I think it's a mistake that Sparkfun puts pull-ups on I²C slave modules. Unfortunately, not everyone who buys modules realizes that excessive pull-up can be a problem. It would be nicer if the controller boards (instead of slave peripheral boards) had pull-ups with solder jumpers.

Oh... Wait... Arduino doesn't carry the (optional) pull-ups (although perhaps it should). So, let's schlep pull-ups everywhere. Easier initial out-of-the-box experience. But add a few slave modules and the bus will stop working.

update (May 2015) :

• Related discussion in comments in another thread.
• In their recent modules, SparkFun began to add solder blob jumpers between Vcc and the I²C pull-up resistors (example). That allows to disconnect the pull-ups more easily.

update (Dec 2015) :
Similar questions about troubleshooting I²C with multiple modules keep popping up on message boards. Attempt at an extended general response.

I, too, once destroyed my Tiva C-series dev board. Maybe the high inductance of motors drew current even when the output stage of the uC pins tried to protect itself. I can't see what is wrong in the picture of the board you posted. You can spend hours debugging this, and perhaps someone knows exactly what you did. However, the board is $25 and ships next day from digikey.