Hi Esc
I have all three OS's installed on their X5000, but in honesty you will need to decide what is important to you when using the machiine on a day to day basis and where.
If 3D is important on Amiga OS then make sure you are using a Southern Islands graphics card (Radeon 7750 or R7 260/270) and forget about Linux or MorphOS at least for the time being. As Christian as pointed out, you can use Linux but you won't be able to benefit from Hardware acceleration. I haven't tried the two graphics card solution he has suggested, however, MorphOS will not support running from a 2nd graphics card.
If you want to use MorphOS, AmigaOS and Linux on the same machine, then consider using either a Radeon 1650 card or a Radeon series 4000,5000 or 6000 series card. Each has their benefits and flaws which I will lay out below:
Use of a Radeon 1650 card will mean you have 3D and TinyGL support in MorphOS and hardware accelration. Support for hardware acceleation is possible in Linux, however as the card only supports up to Open GL 2.0, you will struggle to play 3D games in Linux that require OpenGL 3.0 and above (Super Tux Kart). On AmigaOS 4 forget about any 3D and due to the age and specs of the card, video playback won't be fantastic through MPlayer or Emotion although it is acceptable if you tweak some settings.
Use of a Series 4000 card will mean no 3D support in MorphOS, but you will get 2D hardware acceleration and Overlay, this is important if you like to run emulators or anything than needs an upscaling of the screen from the size of a postage stamp to display in full screen or need to play back any video without serious tweaking. You also lose out TinyGL support in MorphOS which mean that a lot of games that require this will not run. in Linux this should work fine and support hardware acceleration. OpenGL support is up to 3.3 on these types of cards so should run most 3D stuff.
Use of a series 5000 or 6000 card will be the best option for Linux in terms of 3D games performance and video playback. In MorphOS you will lose the overlay which mean that you will struggle to play stuff like PC Engine emulators Hu-Go, Dgen or anything else that requires overlay to display in fullscreen.
The use of all three OS's will require some compromise and again this is down to personal choice about what you will want to use your system for on a daily basis.
It would be nice if all three could support the same graphics card some day and to the same level, but the setups are how they are at the moment until support comes along.
Please do check out the alternative options and decide for yourself if that is something you want to keep, for me it is very much about personal preference and needs rather than one over the other.
I don't know if MorphOS works with a second graphics card.