The total solution for this must be a Linux VCB proxy server. VMware must be developing VCB Framework for Linux... daft not to....but like yourself heard nothing on the horizon... but there is VMWORLD 2008 in Vegas this September...maybe something then...
Linux OS's can read NTFS, FAT etc for your Windows OS, and handles native Linux filesystems ext3, reiserfs etc. Windows only deals with.. well Windows.
And all these products like VEEAM backup and VRANGER all touting File Level Backups of your VM.... yeah Windows Only!
I came to thinking this, only a Windows VCB Proxy server is possible at the moment and you can only do FULL VM backups of Linux VMs, (not file level backups) but why can't you at least mount the the VMDK disk files of the Linux Guest OS on your staging area and if you had drivers for all linux filesystems loaded on the windows vcb proxy server you could see inside you VMDK and copy files out that way.
There is a company http://www.crossmeta.com/crossmeta.html that deals in File System drivers for Linux filesystems on Windows.
P.S. VCB 1.5 is just out and got some interesting fixes. Although part of ESX 3.5 U2, I think you should be able to just install this straight on to your proxy without the need to run the Update 2 on your ESX host.
Looks like this might fix an issue I experience with a large VMDK file (400GB) where it cancelled the snapshot half way through, as disk leases were not being renewed after 5 retries.
Release Notes here:
http://www.vmware.com/support/vi3/doc/vi3_vcb15_rel_notes.html
