What stripe size should I choose for this RAID-5 setup

See, here you err....

lets say both are 64kb, what happens when I run a write operation that's only a few bytes on a section of the drive that's full?(perhaps a large sql server database)

This is not possible.

Besides the fact that NTFS actually has blocks of 4kb or more - and it is STRONLY adviced to set that to 64kb for SQL Server.

SQL Server manages 8kb pages, and always reads /Writes 8 pages as extent - 64kb.

http://msdn.microsoft.com/en-us/library/ms190969(v=sql.105).aspx

As a result, for SQL Server, there is no thing such as writing a few bytes. It will write out 64kb.

As such, for SQ LServer, it is recommended to use a 64kb NTFS node size (so the extends do not cause split IO) and obviously a multiply of 64kb Raid strize size (as enterprise edition of SQL Server loves reading ahead exteds).

For other elements things are similar - not SQL Server... it depends on the intelligence of the programmer and the patterns of access of specific software.

This depends more on what guest OS you intend to use the VHD with than it does on the physical storage subsystem. (In general, with virtualization, you want to separate the physical characteristics from the virtual characteristics, so that you can move your VM from one host to another.)

If your guest OS supports 4K disks, then you'll probably get better performance for a big VHD by using 4K sectors. If your guest OS doesn't support 4K disks, you'll be really frustrated if you use them.

And if the VHD is small, then probably none of this matters much. 4K disks are a much bigger deal when the disk is large.