gksu it is. From #ubuntu-desktop:

11:02:42 < soren> What is the blessed way to run stuff as root from .desktop 
files nowadays?
11:03:01 < soren> ...for something that does not natively support policykit, of 
course.
11:03:05 < asac> soren: i think the idea is policykit
11:03:11 < asac> and if not, there is only the good old way
11:05:58 < soren> asac: And what is that? gksudo? gksu? Something else that 
I've forgotten about?
11:08:13 < asac> gksudo
11:08:16 < asac> but only 90% sure
11:08:40 < asac> we dont have that many apps that need root ... mvo ?
11:25:05 < mvo> asac: no, not that many.
11:25:17 < mvo> asac: still some though
11:25:28 < ~asac> mvo: they use gksudo?
11:25:33 < mvo> yes
11:25:36 < mvo> well, gksu
11:25:41 < mvo> and we default to sudo mode there
11:25:51 < ~asac> soren: see above
11:26:29  * soren nods
11:26:32 < soren> mvo, asac: Thanks.

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zenmap not installed to menus properly
https://bugs.launchpad.net/bugs/461271
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