I know of only two control panels supporting both Windows and Linux platforms simultaneously. One is H-Sphere and the other is Hosting Controller. Which do you think is better in management of multi-platform environments?

Both are, however, Hosting Controller does not have any native application built-in that will port your data from other control panels. Also, software like WHMCS don't support Hosting Controller. Its a good software, but these two issues kept us from using it.

While I do like the Hsphere control panel, its easy to understand and many hidden features are in it already, but its just sad to know that noone can migrate from this control panel to cpanel/plesk along with my web contents.

Both are, however, Hosting Controller does not have any native application built-in that will port your data from other control panels. Also, software like WHMCS don't support Hosting Controller. Its a good software, but these two issues kept us from using it.
Its got its own billing and support system built right into the system. Even if WHMCS or any other billing system doesnt support it, I doubt that should be a reason for not using a software.
Virtuozzo is not supported by WHMCS and hundreds of Companies use both (including us). Same goes with dedicated servers that has to be managed externally using another server.
While I do like the Hsphere control panel, its easy to understand and many hidden features are in it already, but its just sad to know that noone can migrate from this control panel to cpanel/plesk along with my web contents.
HSphere is more of dead system now. After the Parallels takeover of PSoft, all of PSoft's products have gone very, very slow development. Not worth investing any money on it to setup a new cluster.
Try Parallels' new systems. Parallels System Automation or Parallels Business Automation. They are simply mind-blowing (both in terms of pricing and features :P).