The Intel CPU is more powerful.
X79 is the last X chipset to have Windows 2000 (and XP and Vista) drivers. However, by that time, motherboards were already featuring components that don't have Win2k drivers. No motherboards I looked at used USB3 or SATA controllers that have Win2k drivers.
Intel SATA controllers don't have 2000 or XP drivers. (There's a modded driver made by blackwingcat.) Marvell and ASMedia SATA controllers both have only XP (and above) drivers.
Official SATA driver support for Win2K ended at ICH8M. See MSFN thread and bearwindows's site for more information.
The "RocketU 1144A" USB3 board, with an ASMedia controller, works on Windows 2000. (source)
MSFN thread about USB3 on Windows 2000
Below is a table of some X79 motherboards and the support status of their components. Red means it has no drivers for 2000 or XP, yellow means it has drivers for XP (and above) only, and green means it has drivers for 2000 and above.
| brand | model | sata | audio | lan |
|---|---|---|---|---|
| msi | X79A-GD45 | intel | alc892 | realtek |
| msi | X79A-GD65 (8D) | intel+asmedia | alc892 | intel |
| msi | X79A-GD45 Plus | intel | alc892 | intel |
| msi | Big Bang-XPower II | intel+asmedia | alc898 | intel |
| asus | x79 deluxe | intel+marvell+asmedia | alc1150 | realtek+intel |
| asus | p9x79 deluxe | intel+marvell+asmedia | alc898 | realtek+intel |
| asus | p9x79 le | intel+asmedia | alc892 | realtek |
| asus | p9x79 pro | intel+marvell | alc898 | intel |
| asus | p9x79 ws | intel+marvell | alc898 | intel |
| asus | p9x79 | intel | alc892 | intel |
| asus | RAMPAGE IV BLACK EDITION | intel+asmedia | ? | intel |
| asus | Rampage IV Extreme | intel+asmedia | alc898 | intel |
| asus | Rampage IV Formula | intel+asmedia | ? | intel |
| asus | Rampage IV GENE | intel+asmedia | ? | intel |
| asus | sabertooth x79 | intel+marvell | alc892 | intel |
| asus | x79 deluxe | intel+marvell+asmedia | alc1150 | realtek+intel |
| gigabyte | ga-x79-ud3 | intel+marvell | alc898 | intel |
| gigabyte | ga-x79-ud5 | intel+marvell | alc898 | intel |
| gigabyte | ga-x79-ud7 | intel+marvell | alc898 | intel |
| gigabyte | ga-x79-up4 | intel+marvell | alc892 | intel |
| gigabyte | ga-x79s-up5-wifi | intel | alc898 | realtek+intel |
| asrock | x79 extreme9 | intel+marvell+asmedia | ? | broadcom |
| asrock | x79 extreme7 | intel+marvell | alc898 | broadcom |
| asrock | x79 extreme6/gb | intel+asmedia | ? | broadcom |
| asrock | x79 extreme6 | intel+asmedia | alc898 | broadcom |
| asrock | x79 extreme4 | intel+asmedia | alc898 | broadcom |
| asrock | x79 extreme4-m | intel+asmedia | alc898 | broadcom |
| asrock | x79 extreme3 | intel+asmedia | alc898 | broadcom |
| asrock | fatal1ty x79 professional | intel+marvell | alc898 | broadcom |
The drivers for Sandy Bridge (x6x) and Ivy Bridge (x7x) chipsets (LGA 1155, which doesn't include the Extreme CPUs), version 9.x, still support Win2k (except SATA and onboard graphics drivers, which only support XP and above). The best LGA 1155 CPU is i7-3770K. The best chipset in the x6x and x7x series is the Z77. Among the Z77 motherboards by ASRock, Extreme3, Pro3 and Pro4 use Realtek network controllers which have Win2k drivers. You will have to use IDE mode for hard drives, and use a discrete graphics card (which is the better choice anyway). i7-3770K is also the best non-extreme CPU for XP and Vista.
Another interesting motherboard by ASRock is the H61M-IDE, which AFAIK is the last motherboard to include IDE ports. H motherboards don't permit full overclocking or using multiple graphics cards, though.
As for the CPUs themselves, see the comparison. 990X is worse at single thread but better at multi thread than 3770K.
This is the previous generation of extreme CPUs, with the Intel X58 chipset. It still doesn't have SATA drivers for Win2k, but does for XP. Asus Sabertooth X58 is a motherboard that would probably work.
X99 seems to be popular on MSFN for builds with modded drivers.
MSFN thread, VOGONS thread, hardforum thread
The 3 ASRock boards I listed are the only ones I can find that still support Windows 2000 with this CPU.
While there are newer CPUs both for AM3 and in the Phenom II X4 series, none of those CPUs are supported by a chipset that still supports Windows 2000.
The Nvidia GPU is more powerful.
The last driver version to support 2000 is 258.96, although Nvidia only lists XP and up as supported OSes. This is stated on multiple websites. The most powerful GPU supported by this driver is GTX 480.
The last driver version to support 2000 is 6.5 (release notes). The most powerful GPU supported by this driver is X1900 XTX. However, because the last version that supports X1900 doesn't support Windows 2000, AMD's download page doesn't mention Windows 2000.
Modded drivers are available for ATI Radeon 9xxx/X300~X2100 and HD2000~6000. (MSFN thread)
The last Sound Blaster sub-series to have Windows 2000 drivers is Audigy. However, XP drivers for X-Fi can be installed by modifying the configuration file.