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I'm curious, if one can upgrade the security Skype offers to avoid a man in the middle snooping in on the calls by both parties using a client side plugin? Does one exist for this purpose?

A bit of background reading:

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Skype already does that. – Adi Jun 6 '13 at 21:54
Skype has a backdoor for the FBI. So no I do not trust their implementation – Charles Hoskinson Jun 6 '13 at 21:55
Then use – Adi Jun 6 '13 at 22:04

No, there isn't any plugin for Skype that would plug into its transport layer and custom encrypt calls peer-to-peer, and there likely won't be any as:

Skype uses a closed proprietary protocol, which they do not publish. Skype intentionally does not interoperate with the rest of the VoIP industry, which is built on open standards. [1]

Skype is now fighting back to regain its reputation and end users' trust, after the series of news stories, such as you link to, have alleged that: Skype changed its network's architecture since its acquisition by Microsoft last year to enable “lawful interception” of calls.

Mark Gillett, Skype COO:
"Skype to Skype calls do not flow through our data centres and the "supernodes" are not involved in passing media (audio or video) between Skype clients. These calls continue to be established directly between participating Skype nodes (clients). In some cases, Skype has added servers to assist in the establishment, management or maintenance of calls."

Well, right. Managed calls anyone?!

TL;DR - Since Skype is using a proprietary hybrid TLS (combining both client-server and peer-to-peer encryption protocols, and not that safe ones at that either), I don't see them opening up to the wider VoIP community and supporting custom encryption schemes and ZRTP.

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Is there a VOIP you would recommend that does present my requested features? – Charles Hoskinson Jun 7 '13 at 5:35
@CharlesHoskinson - It's hard to give any direct recommendation not knowing your requirements. You could investigate your options on your own by starting with this Comparison of VoIP software. Honestly though, short of cashing out for some paid solution the choice is rather limited, if A/V is a requirement. Personally, I use Google Talk w/ video chat plugin (alternatively, you could try Hangouts) in OTR mode, but not for highly confidential stuff. :? – TildalWave Jun 7 '13 at 6:49

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