The VoxBo package has two overlap-related tools. vbmaskcompare produces a handful of metrics, although I foolishly didn't include Dice overlap (it's easily computed from the values it does produce, I'll add it explicitly soon). It also includes the discrepant voxel count metric from Fiez et al., and there are hooks for the surface comparison metric used in that article as well, although it's not currently in the code because it slowed things down too much. If there's interest, I'll optimize it and put it back in. I do need to optimize the whole thing because the discrepant voxel count is already too slow (can run over a minute).

http://voxbo.org/index.php/vbmaskcompare

We also have a tool for printing a table of overlap measures with the regions in an atlas (e.g., all the regions in the AAL atlas that are impinged by a lesion). Doesn't sound like that's what you meant, but just in case, here's a link:

http://voxbo.org/index.php/vboverlap

Both these tools are in active development (new versions will be released next week, and probably the week after as well), so feel free to request features you'd like to see. The functionality from both will also soon be folded into another program, more of a swiss army knife along lines similar to the program John Pluta mentioned:

http://voxbo.org/index.php/vbimagemunge

All are available for Linux and OSX, and there are older versions available for Cygwin as well. Should compile on Solaris if there's interest, but I have no Solaris box to try it.