This patch series should solve most color problems with different drivers:
http://patchwork.ozlabs.org/project/qemu-devel/list/?series=124472
Some endianness issues may still remain, however those may be bugs in the Linux driver now. This should be confirmed by checking against real hardware as some drivers are known to have similar problems on PowerPC machines at least.
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Other than 8 bpp modes may have wrong colors with Linux frame buffer driver, e.g. with aty128fb on x86_64 host and guest the default 8 bpp mode is OK but issuing
fbset -g 1024 768 1024 768 16
causes colors to disappear, with 32 bpp everything is black. Not sure if this is a bug in Linux framebuffer driver or ati-vga emulation though.
Emulating PPC machine on x86 host also may show wrong colors in more than 15 bpp modes with Linux guest (but seems to work with MorphOS).