I'm running Debian Squeeze (x64):
# uname -srvmo
Linux 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux
I have 2 compatible 2 GB sticks of DDR2 in my G31M-S motherboard. It supports up to 8GB:

Since this is a server, I don't really care about graphics. So I set it to the lowest.
Internal Graphics Mode Select: Auto
Enabled, 1MB <--
Enabled, 8MB
DVMT Mode Select: Fixed Mode <--
Auto
DVMT/FIXED Memory: 128MB <--
256MB

However, Linux is only detecting 3.19GiB of memory:
# cat /proc/meminfo
MemTotal: 3350712 kB
...
Looking at the E820 map:
[ 0.000000] BIOS-provided physical RAM map:
[ 0.000000] BIOS-e820: 0000000000000000 - 000000000009f800 (usable)
[ 0.000000] BIOS-e820: 000000000009f800 - 00000000000a0000 (reserved)
[ 0.000000] BIOS-e820: 00000000000e6000 - 0000000000100000 (reserved)
[ 0.000000] BIOS-e820: 0000000000100000 - 00000000cfdb0000 (usable)
[ 0.000000] BIOS-e820: 00000000cfdb0000 - 00000000cfdc0000 (ACPI data)
[ 0.000000] BIOS-e820: 00000000cfdc0000 - 00000000cfdf0000 (ACPI NVS)
[ 0.000000] BIOS-e820: 00000000cfdf0000 - 00000000cfe00000 (reserved)
[ 0.000000] BIOS-e820: 00000000fed00000 - 00000000fed00400 (reserved)
[ 0.000000] BIOS-e820: 00000000fee00000 - 00000000fee01000 (reserved)
[ 0.000000] BIOS-e820: 00000000ff380000 - 0000000100000000 (reserved)
[ 0.000000] DMI present.
[ 0.000000] AMI BIOS detected: BIOS may corrupt low RAM, working around it.
[ 0.000000] e820 update range: 0000000000000000 - 0000000000010000 (usable) ==> (reserved)
And doing a little math:
>>> ((0x9F800 - 0x10000) + (0xCF6B0000 - 0x100000)) / 1024.0 / 1024.0 / 1024.0
3.240476608276367
We get just about the same answer.
What am I missing?
I'm not completely buying the "PCI address space" argument. Taking one of the two 2GB sticks out, the setup screen shows 2048MB.
# cat /proc/meminfo
MemTotal: 2058432 kB
That's 1.96GB.
E820 map again:
[ 0.000000] BIOS-provided physical RAM map:
[ 0.000000] BIOS-e820: 0000000000000000 - 000000000009f800 (usable)
[ 0.000000] BIOS-e820: 000000000009f800 - 00000000000a0000 (reserved)
[ 0.000000] BIOS-e820: 00000000000e6000 - 0000000000100000 (reserved)
[ 0.000000] BIOS-e820: 0000000000100000 - 000000007fdb0000 (usable)
[ 0.000000] BIOS-e820: 000000007fdb0000 - 000000007fdc0000 (ACPI data)
[ 0.000000] BIOS-e820: 000000007fdc0000 - 000000007fdf0000 (ACPI NVS)
[ 0.000000] BIOS-e820: 000000007fdf0000 - 000000007fe00000 (reserved)
[ 0.000000] BIOS-e820: 00000000fed00000 - 00000000fed00400 (reserved)
[ 0.000000] BIOS-e820: 00000000fee00000 - 00000000fee01000 (reserved)
[ 0.000000] BIOS-e820: 00000000ff380000 - 0000000100000000 (reserved)
[ 0.000000] DMI present.
[ 0.000000] AMI BIOS detected: BIOS may corrupt low RAM, working around it.
[ 0.000000] e820 update range: 0000000000000000 - 0000000000010000 (usable) ==> (reserved)
And the math...
>>> ((0x9F800 - 0x10000) + (0x7fdb0000 - 0x100000)) / 1024.0 / 1024.0 / 1024.0
1.9973125457763672
So I got 2GB / 2GB. /proc/cpuinfo shows that my processor supports 36-bit physical addressing. 2^36 = 64GB, which I'm not even close to.
# ./smem -R 4G -w
Area Used Cache Noncache
firmware/hardware 843592 0 843592
kernel image 0 0 0
kernel dynamic memory 181116 134616 46500
userspace memory 287784 19736 268048
free memory 2881812 2881812 0