PulseAudio vs ALSA
Linux has two different audio systems, these are PulseAudio and Advanced Linux Sound Architecture (ALSA).
If you have a PC that is exclusively used for XBMC then using ALSA maybe the best solution, for more background refer to Advanced Linux Sound Architecture
If you have a PC runs many applications other than XBMC then using PulseAudio maybe the the best solution, for more background refer to PulseAudio
To help you decide which is best for you these are the various use cases:
PulseAudio FAQ
Known issues
Configuring PulseAudio
When using PulseAudio some configuration at the OS level maybe necessary to get audio from XBMC.
For how to do this refer to PulseAudio
Hardware Vendor Specifics
AMD
For AMD GPU's there are two sets of drivers available, the AMD supplied binary fglrx drivers or the newer Radeon OSS drivers.
fglrx Drivers
The AMD fglrx drivers on Linux limit the number of real audio channels to 2.0, this only provides enough bandwidth for LPCM 2.0, DTS (5.1) and AC3 (5.1) and so HD audio (DTS-HD, TrueHD) is NOT possible on Linux for AMD GPU's using the fglrx drivers, further to this the fglrx drivers limit HDMI audio to a 48Khz sample rate however 96KHz is possible on SPDIF.
The AMD developers responsible for the fglrx drivers have failed to provide any updates or improvements to the XvBA hardware acceleration API that the drivers use for more than 2 years, meaning no AMD fglrx driver since 12.10 has been usable.
Radeon OSS Drivers
As a consequence of the lack of XvBA updates, XBMC's developers got in contact with the AMD OSS developers to see what could be done to improve AMD graphics in Linux, the result was the Radeon OSS drivers which have been developed to use the open source VDPAU API.
The Radeon OSS driver are now more feature rich and better performing than the fglrx ever were, amongst other things they are capable of allowing HD audio (DTS-HD, TrueHD) to be bitstreamed.
For more detail see forum thread Linux - Radeon OSS with vdpau (howto)
Intel GPU HD Audio
HD Audio on Intel SandyBridge & IvyBridge systems require a patch from Intel to be included within the kernel, Linux 3.7 and higher include this patch as standard. In addition modification to system files maybe required in order to get the HDMI audio working.
For more detail on the required Linux modifications see Intel Linux Modifications for HD Audio