I think there is no reason to go to 5.0 unless you need SIP feature set on the line side. (phones). 5.0 callmanager follows the same feature set as 4.1(3) plus a few additional functions like Presence. CM 6.x (6.0, 6.1) when it comes out in spring 07, will possibly give you the option to run on linux or windows, plus a tonne of new features.
We recommend 4.1 or 4.2 to most clients at this moment, unless specific requirements trigger the recommendation of 5.0.
5.0 has been pretty stable for us. No weekly or semi-weekly reboots to deal with memory leaks in MS SQL.
As of 5.0(4) there are small issues with memory leaks in the CCM service if you have moderate numbers of phones the repeatedly re-register (wan outages), but restarting CCM is easy and fast. Oh, and multicast MoH doesn't stream to gateways unless a MTP is forced (4.X did not require this)
Otherwise I couldn't be happier having moved to 5.X as soon as it was available.
5.0 is a dead train, as soon as you'll open a TAC case they'll tell you to go to 5.1. Unless you need an appliance model, SIP phones, or Presence server you don't get much more out of 5.X.
Off course 5.1 is brand new and you never want to be an early adopter.
I have couple of customers that I am doing a design for and they insist on 5.X release, because that what local Cisco Team has been pushing, but they are not the ones implemeting it and dealing with software bugs. I still recommand 4.1 or 4.2 if the feature are required to all customers. But ultimiately it's their environment and decision, I can only do so much :-)
If you do not need SIP simple I would recommend 4.2 at this moment, and definately not 5.0 nor 5.1 since 5.0 was developed with feautures that where in 4.1
6.0 should be released in Q1 (provider/enterprise market pressure), it is expected that 6.1 will follow in Q2 as 6.0 might not have all features (Cisco will just disable features that are not proofed stable before they launch 6.0)
For now, recommend 4.2 to customers that do not require any of the 5.0 specific features and recommend them to wait with upgrading untill 6.1 is launched
6.0 will support both Linux and Windows OS as far as I understood :-))
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Topology: IP Phone > Switches > Microsoft NPS setup to forward 802.1x
proxy to > ISE 2.1 patch 3 Authentication: EAP-TLS using Cisco MIC SANs
Phone Models 802.1X support? 802.1x flavor Addtl Comment EAP-MD5 EAP-TLS
Cisco 3905 Y Y N Cisco 6911 Y Y N Cisco ...