I did a little bit of research into the problem of mkdepend.exe being slow under VMWare with sources in VMWare's shared file system.
The first thing to do was to measure the problem. This was pretty easy: running mkdepend on nsPresShell.cpp consistently takes 32 seconds. Actually compiling the file takes only a few seconds. So clearly something is very wrong.
Poor-man's profiling in the debugger shows that mkdepend is spending all its time in stat() calls. These stat calls are just checking to see whether a file exists; on a hunch I wondered if there's a faster way to check for file existence than stat(). Some Web searches suggested that GetFileAttributesEx is a good fast way. So I refactored the code to use a does_file_exist function which calls GetFileAttributesEx on Windows. Ta da! Now mkdepend on nsPresShell.cpp takes 1.5 seconds. GAME OVER. Patch submitted.
I conjecture that stat() is so slow because it fills in a bunch of information about devices, inode numbers, and access permissions, and on Windows that may require several filesystem operations to get that information. Perhaps VMWare's file system is particularly slow at some of those extra operations.