At this time, Wubi does not work with Windows 8 default boot-loader. Thus at this point Wubi would not work on a new Windows 8 machine.
Citation fom WubiGuide
Recently I've learned of Wubi, a way to install Ubuntu right from Windows.
Besides installing from Windows, I would like to know key differences between a regular "alongside Windows" or Dual-boot Ubuntu installation and one done with Wubi. Are there any disadvantages (for example a performance penalty) or incompatibilities I should look out for when using Wubi?
You can expect disk performance to be a bit lower (bouncing through NTFS isn't exactly ideal), and you're still somewhat at the mercy of Windows. If your Windows install goes pear-shaped, you may lose access to your Wubi install, too. The reliance on NTFS would also give me heartburn in general, but that by itself probably won't be a serious reliability problem.
Other than that, I can't think of anything that should be different. If you do find a problem, report a bug! :)
There is one other catch noted on the Wubi FAQ in addition to performance/reliability: Hibernation isn't supported.
(I'll note for the record, however, that even with native installs, I've rarely had reliable suspend or hibernation support in any Linux distribution, including Ubuntu.)
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