According to AnandTech, Intel's first Thunderbolt controller chip is codenamed Light Ridge. This part, L051NB32, is what you will find in most other Thunderbolt-equipped Macs. It can support up to four bi-directional 10Gbps channels (or 80Gbps total) and up to two DisplayPort output channels.
However, Intel has a second Thunderbolt controller code named Eagle Ridge. This part, L123TA46, comes in two packagesone is like the standard packaging used for Light Ridge, and the other is a slim, SFF package. It can support two bi-directional 10Gbps channels and just one DisplayPort channel. It is essentially, as AnandTech describes it, "half of a Light Ridge chip."
Eagle Ridge's single DisplayPort channel is part of the reason the new MacBook Airs can only support one external display. Since the 13" MacBook Pro also only supports one external display, despite the higher-end Thunderbolt controller, the Intel HD 3000 also appears to be a limitation as well.
It's worth noting that a single Thunderbolt port only uses two bi-directional channels, so machines that don't need to support more than one external display and only have one Thunderbolt port could use easily use either version of Eagle Ridge.