How to deal with multiple pull-up resistors on modules
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.