I am looking for a modern system to do some bare bones Assembly programming (for fun/learning) that does not have the legacy burden of x86 platforms (where you still have to deal with BIOS, switching to protected mode, VESA horrors to be able to output pixels to the screen in modern resolutions/colordepths etc.). Do such systems even exist? I suspect it is not even possible today to do low-level graphics programming without dealing with proprietary hardware.
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qemu is likely what you want if you dont want to have to build that stuff in. You wont get as much visibility as to what is going on in the guts of it.
For hardware, beagleboard (dont get the old one get the new one with reasonable connectors, etc), or the open-rd board. I was disappointed with the plug computer thing. The hawkboard I like better than the beagleboard, but am concerned about the big banner about a pcb design problem. The raspberry pi will be out at some point and will also provide what you are looking for. Note that for beagleboard, etc, you dont have to run linux or anything like that, you can write your own binary and xmodem it over or use the network and then just run it, not a problem at all.
The stellaris eval boards all/most have oled displays, monochrome and small but graphics, not sure how much you were after.
earth-lcd used to have an arm based board with a decent sized panel on it.
there is of course the gameboy advance and the nintendo ds. flash/developer cartridges are under $20. the gba is better to start with IMO, as the nds is like two gbas competing for shared resources and a little confusing. with a ez flash cartridge (open source software to program), was easy to put a bootloader on the gba and for like another $20 create a serial cable, I have a serial based bootloader for loading the programs. If you have an interest in this path start with the visual boy advance emulator to get your feet wet and see how you feel about the platform.
If you go to sparkfun.com there are likely a number of boards that either already have lcd connectors that you would mate up with a display or definitely displays and breakout boards that you could connect to a number of microcontroller development boards. Other than the insanely painful blue leds, and the implication that there is 64KB (there is but non-linear 32KB+16+16) the mbed board is nice, up to 100mhz, cortex-m3. I have some mbed samples at github as well that walk you through building an arm binary too boot an arm from flash for those that have not done it (and want to learn that rather than call some apis in a sandbox).
the armmite pro and the maple (sparkfun) are arm based arduino footprint platforms, so for example you can get the color lcd shield or the gameduino
There is the open pandora project. I was quite dissappointed with the experience, after over a year paid another fee to get the unit and it failed within a few minutes. Sent it back and I need to check my credit card statement, maybe we took the return and give it to someone who wants it path. I have used the gamepark gp32 and gpx2, but not the wiz, the gpx2 was fine other than some memory I/O problem in the chip that caused chaotic timing. the thing would run just fine but memory performance was all over the map and non-deterministic. the gp32 is not what you are looking for but the gpx2 might be, finding connectors for a serial cable might be more difficult now that the cell phone cable folks used to cut up is not as readily available.
gen 1 ipod nanos can still be had easily, as well as the older gen ipod classics. easy to homebrew, the lcd panels are easy to get at. grayscale only, maybe only black and white I dont remember. All the programming info is had from the ipodlinux folks.
I have not tried it yet but the barns and noble folks are homebrew friendly or as friendly as anyone on that scale has been so far. the nook color can easily be turned into a generic android device, so I assume that also means you could develop homebrew on the metal, not sure though, have not studied it.
You might look at always innovating, my experience with them was similar to the open pandora folks. These folks started with a modified beagleboard in a box with a display and batteries, then added a couple more products, any one of them should be very open, and homebrew friendly so you can write whatever level you want, boot and run on the metal, no problem. For the original product it was one of those wait for several months things.
I am hoping the raspberry pi becomes the next beagleboard but better.
BTW all hardware is proprietary, it is just a matter of whether they choose to provide programming information or not. vesa came about because no two vendors did it the same way, and that has not changed, you have to still read the dataseets and programmers reference manuals. But as you can see above I have only scratched the surface, and covered the sub or close to $100 items. If you are willing to pay in the thousands of dollars that greatly opens the door to graphics based development platforms that are well documented and relatively sandbox free. many are arm based since arm is the choice for phones, etc and these are phone-like, tablet-like, eval platforms.