I never did get atftpd working properly, but it turned out I was using the wrong command for tacacs+ in Linux Mint. It's actually "tac_plus" (minus the quotes, obviously). Radius also works well, it just requires a lot more setup work than using the 2008R2 for that. It's almost a no brainer in 2008R2.
So far, I've gotten Windows 2008R2, Haiku, Linux Mint 17, Netware 5.1, Windows XP (using IP Blue softphones and Solarwinds TFTP) and an NT4 workstation with the client32 and nwadmin (minus IPX/SPX) working swimmingly in my topology, along with turning a 3745 into a CME for the soft IP phones. So far, a very happy camper! :)
I just wish I could get a 6500 Cat working (for private vlans), but I understand the issues with getting that to work (custom ASICs and all that). I ended up getting a different simulator to practice with that.
*EDIT*
BTW,
here's an article from Cisco support about configuring the CME device via the CLI. Hope this helps anybody else who might be having problems. And you *definitely* need to use the format/flash technique mentioned
in this post, as well as edit the memory, nvram, pcmcia, exec area, and hypervisor settings, or it *will* fail on your first attempt without it.
*EDIT2*
Also, PRTG installs just fine on 2008R2, and works great. I was able to monitor all devices in the topology (SNMP traps, utilization, netflow/sflow, etc...) from both the Haiku VM and Mint17 VM via their web browsers. Make sure you DON'T install IIS7, or it'll cause PRTG admin and console to never start, due to errors with IIS7.