You don't BUY a mainframe for this...
...you already have one. (or really, not less than 2, as buying 1 frame is almost never done...)
If you already HAVE a few frames, because you need to run many DB2 databases, have lots of legacy code, or whatever. Lets say you've licensed 4,000 mips on each, and have lots of spare capacity. Now, adding some IFLs to run Linux is not only easy, it;s cheap, and adds to no other infrastructure.
But lets go with your base assumptions, a completely new mainframe chassis (2 actually) vs enough VMWare nahalem chassis not just to run the guests, but to also add VMotion and enough additional redundant chassis and SAN storage to handle full failover of a datcenter. (If you have enough guests to warent a mainframe, you probably already have more than 1 datacenter in your building, and if you don;t, it;s a REAL good idea you look at your infrastructure redundancy design...)
Lets also look at a few other details your cost analysis missed:
Storage: In the mainframe, hundreds of Linux "guests" can use a single binary image. Hundreds of VM ware guests needs hundreds of times the base OS image storage. Yea, you need data storage, but that's the same price either way, but a 5GB OS image on the mainframe compared to 0.5TB on 100 linux guests is a HUGE difference. (since the base frame has all the I/O components and dedicated I/O processors you'd need, you're just basically buying DAS storage, but for the VM Ware systems, it;s SAN for you...)
DR: (goes to storage as well). On VMWare, your 100 guests need significant storage either on tape or disk for backups. On the mainframe, just a base copy is all you need to back up, plus the differrencing data. There's also no licnecing needed to do this on a mainframe, but each of your 100 linux guests in VM ware needs a backup agent and so does the VM Ware host.
Software (honestly, this is the biggest one!): Lets look at Websphere, Oracle, or any number of other apps you need to buy for these linux guests. On the Host side, 1 "processor" license covers the entire IFL. 5 websphere licences (at 120PVUs each) covers all 5 engines, and hundreds of Linux guests. In VMWare, each of those processors is 120PVUs (if you're talking nahalem xeons). A single rack chassis costs almost as much to license as the whole mainframe... Add to this MQ, DB2, antivirus, scanning and remediation clients, monitoring clients, and more that the mainframe basically either takes care of already, or simply doesn't need).
VMWare itself: Ouch thats's expensive... how many cores did you license it for on the small boxes? including enterprise support, HA, vMotion, storage replication (you do plan on having more than 1 SAN chassis, right, and are not putting 10-20TB of mission critical system images on one bot that could take 3-4 days to recover with even the best DR solutions, right?), management software, and more?
Switching/routing: Mainframe, just needs a few 10Gs to connect to the network. Multiple VMWare chassis? lots and lots of cabling, inband and out of band VLan configurations, fully redundant rack to rack cabling and switching, not to mention the HBAs, SAN fiber switches, and more...
memory: Yes, mainframe memory is nearly $2,000 per GB. Of course, the base frame comes with some significant memory (128GB i believe), and each IFL adds to that. But again, single binary imaging allows a very small memory footprint change per additional guest. We're adding between 64 and 128MB of active memory footprint per additional guest. on VMWare you're likely adding 1-2GB if not more. Sure, you can get 2GB kits dirt cheap, but with only 8 or 12 memory slots, that's not getting you far. Likely you'll be buying 8G and 16G kits, which do not scale linearly in price so well... and the frame has a good head start....
We've been deploying zVM for about 3 years. Upper management CONSTANTLY looks at each new project to compare costs. We actually look at everything I metioned above and more to make our determineation to deploy new or upgraded systems on zVM, VMWare, BlaceCenters, or standalone boxes. If the software runs on zVM (keeping in mind it's not linux, but Linux for OS390X hardware platform, which is a seperately compiled version of Linux, hence the no-need-for-antivirus position), it is ALLWAYS cheaper than VMWare (usually by half or more), and in some cases we've seen a 10 fold savings (especially when dealing with per core or per guest licence models).