I was being a tad bit generic when talking about stacking. Basically, to fit things inside that small of a package, there are some things like DRAM stacked to make space for more radios, and the PCB is thicker. I'll let Anandtech get specific: AnandTech - LG Optimus 2X & NVIDIA Tegra 2 Review: The First Dual-Core Smartphone
In the smartphone space, the integration is even more pronounced. With physical space and power as major constraints, smartphone chip makers have been forced to further trade performance for integration. The level of integration is so high within a smartphone that you almost never hear about what CPU a phone uses, but rather what Application Processor it uses otherwise known as an SoC (System on Chip or System on a Chip).
Package on Package (DRAM on top, SoC on bottom)—source: statschippack.com
Integrate a CPU, GPU, memory controller, video decoder, audio decoder, video encoder (sometimes), camera processor, system memory and maybe even a modem onto a single chip and you’ve got something that can only be described as a System on a Chip. It’s a single physical chip that integrates nearly all of the functions of the entire computer. Nearly all of the aforementioned components are on a single piece of silicon, with the exception of any integrated memory. To save board real estate and enable smaller form factors, it’s not uncommon to stack DRAM on top of the SoC package instead of beside it. The SoC in a PoP (Package on Package) stack has contacts on its top surface that line up with the balls on the DRAM for power and signaling. PoP stacks work because the SoC underneath doesn’t dissipate much heat and thus doesn’t mind being insulated by some DRAM up top.
If we look at the Thunderbolt's thickness, it's because they packed in dual radios (for 3G data & voice) plus an LTE radio:
So the PCB had to be longer, making the device have to be thicker in order to include the battery over the top of the PCB, instead of alongside it.
Brandon
Thanks for the info!