BuildCraft writes it's configuration options in the ./minecraft/mods/config/buildcraft/main.conf file. This file contains all assigned Block and Item IDs (which can be changed by the user), as well as a number of other, lesser-known configuration options.
Currently, there are options to:
Allow machines to be driven by continuous current.
Prevent fillers from dropping blocks.
Make Filler destroy blocks instead of breaking them.
Change the lifespan (in ticks) of items dropped on the ground by pipes and machines.
Prevent BuildCraft from generating custom blocks (e.g. Oil).
Change the delay between full client sync packets; increasing it saves bandwidth, decreasing allows better client synchronization.
Decrease network update frequency, which is useful for overloaded servers.
Deactivate pipe connection rules. This is actually deactivated by default, as of 3.4.0, but can be enabled by changing "false" to "true".
Change how long a pipe will take to break.
Change the number of objects in a pipe required for items to be automatically grouped together.
Change the amount of items that a pipe has to contain before it will explode, causing it to not drop any items.
Disable energy loss over distance on all power pipes.