@OP
OS4.x compatible systems:
1) Amiga + Blizzard/Cyberstorm PPC
Compatible with AmigaOS4.x for classic (developed as a seperate release from AmigaOS4.x)
Not guaranteed to be supported by latest OS release, so you may be left lagging behind. In the long term, has to be a boat anchor to development and testing.
Not all (useful) hardware supported - Blizzard PPC scsi chip being one, so you may be left using slow internal IDE bus.
The slowest of AmigaOS supported hardware, but the last real "Amiga".
Will almost certainly not support latest Linux releases.
Will run AROS
Will run MorphOS with a supported RTG card (2 hour time limited demo version, not currently possible to register).
2) AmigaONE SE (G3)
Dreadful, slow, buggy. Avoid.
The slowest 'NG' hardware. A few people have got them running relatively stably, but it's not going to be an easy experience.
3) AmigaONE XE (G3/G4)
Seem to be a lot more stable, although ymmv with a particular board.
The best (or at least the most numerous, resulting in a higher number of 'good' boards) of the Eyetech AmigaONE boards produced.
Good expandability (4? PCI slots), depending on mods made to the board you MAY be able to use a PCI>PCIe adapter and RadeonHD cards*.
Onboard ATA may need to be limited to PIO modes, onboard USB may not work, can be replaced with PCI cards.
4) micro AmigaONE (G3/G4)
Seem to have more problems than the XE, limited expandability, has onboard graphics (Radeon M9/32MB VRam iirc).
Discuss with uA1 owners for more detail on various issues/quirks.
5) Pegasos 2 (G3/G4)
Similar features to AmigaONE XE, but without any of the problems. Stable as hell in fact.
Supports AGP graphics cards.
Onboard Gigabit ethernet (not sure if supported by AmigaOS) and Firewire 400 (not supported by AmigaOS).
Also runs Linux, Mac-on-Linux, MorphOS, etc (Not sure of AROS support).
6) Sam440ep / flex
Well supported by AmigaOS, but weak cpu.
Flex model has good expansion (PCI), plain ep model less so.
Can be bought new for low** cost (
7) SAM 460 (aka AmigaONE 500 when sold in a case)
Better CPU (G4 class, but no altivec iirc)
Good expandability (PCIe x 4 (x16 physical connector for GFx cards), PCIe x 1, PCI x 1
Expensive, but shiny and new.
Onboard audio had several problems, mainly soved through driver updates, but also a manufacturing error (missing resistor) on the audio subsystem on some (not all) individual units. Not sure if all audio problems are entirely soved yet, check with Metalheart and others on AW.net for more info. Can be easily worked around with audio PCI card.
Onboard SATA is mutually exclusive with onboard PCIe x 1 slot (only one can be in use - pick your poison).
Has limited onboard graphics (SM502)

AmigaONE X1000
Powerful (~G4-G5) cpu (Multiple cores/64-bit modes supported in Linux, but not in AmigaOS 4.x at all).
Good expandability (2 x PCIex16 graphics slots (only 16 lanes assigned - can be 1 x 16x, or 2 x 8x) , 2 PCIe slots, 2 PCI slots.
Onboard USB2.
Has Xena (use yet to be determined) bolted to CPU GPIO lanes (use-case for this high-speed, low-latency interface is yet to be determined), and to Xorro slot. Xorro slot can be fitted with an I/O board to present interface outside the case (again, usefulness yet to be determined).
Seem to be a very stable board, although PCI bus is shockingly slow (possibly lack of DMA in AmigaOS4 PCI drivers on this board) so even using a PCI based graphics card may be very slow.
Frankly, were I determined to buy an AmigaOS compatible board, I'd go for the Peg2, Sam440, the X1000 or the SAM460.
Not bothered about having a new board? Peg2 - best all-rounder, most stable G4 board, has altivec.
Just to test compatibillity/play around with as a curiosity? Sam440
As an AmigaOS4.x main machine at a reasonable** price? Sam460
As a dual-booting useful Linux workstation capable of doing some real number crunching/high memory applications, which also runs AmigaOS4.x? X1000
The new boards have companies behind which will give you good hardware support (A-Eon, A-Cube). The Peg2's have had fantastic hardware support for nearly a decade, but are not under any warranty. Eyetech boards aren't in any way supported, although you may be able to get repairs/hardware-mods performed by 3rd parties.
Hardware assessed, I would also base my decision on what is supported RIGHT NOW in AmigaOS, not what has been implied/promised/bet-it-won't-take-two-years'ed.
The last few years have shown how little Hyperion can be relied upon to pull their weight with respect to moving AmigaOS forward, as nearly all progress has been either 3rd party (funded by A-Eon mainly), or community volunteers gaining access to continue elements of OS development (Lyle Hazlewood, Fredrick Wistrom).
Multi-core? Gallium 3D? I'll believe it when I see it _working_.
Open-office? Warp3D? Much more of a chance of appearing, as it's a 3rd-party effort funded by Trevor.
* RadeonHD cards are currently supported in 2D only (Respect to Hans's 2D work, which seems to function well from what I have read (haven't used myself)). Hardware video scaling on these cards requires 3D drivers, which are dependent upon Hyperion's Gallium3D work, which has been some years and appears to have made little progress.
Consequently, video playback performance on these cards really sucks, so until/if/when/somewhere-over-the-rainbow 3D drivers arrive (and video scaling via textures) you're probably better off sticking with a Radeon 9xxx if you want to be able to watch videos or play 3D games.
** Used in the relative sense.