It can be changed via commandline [1]:
ftype bitcoin
to see what the current setting is.
with
ftype bitcoin="C:\Program Files\Bitcoin\bitcoin-qt.exe -datadir=d:\mybitcoindata\is\here" "%1"
it should do what you want. Another possibility would be to do it via the registry [2], but ftype should change the same registry key anyway.
[1] source: http://stackoverflow.com/questions/796748/how-can-i-add-a-custom-url-handler-on-windows-like-itunes-itms
[2] as linked from [1] http://msdn.microsoft.com/en-us/library/aa767914%28VS.85%29.aspx