Don’t know why I didn’t know this already! . . .
If you have Message Tracking enabled on your Domino servers then the MTC will maintain a Full Text index on the MTSTORE.NSF, but this FT index accumulates a lot of dead space.
You can reclaim the dead space by adding “MTCCompactReIndex=1” to the NOTES.INI (recommend you do this from a Configuration Settings document in the NAB), so a daily re-index will be executed when MTC does its daily maintenance. I just did this on our 8.5.1 servers and FT indexes that were in the 2 - 4GB region shrunk overnight to 2 - 600MB!
Have a look at these for more information:
1. Technote "Does MTC require mtstore.nsf to be indexed?": http://www-01.ibm.com/support/docview.wss?uid=swg21206693
2. Wiki "MTCCompactReIndex": http://www-10.lotus.com/ldd/dominowiki.nsf/dx/mtccompactreindex
Perhaps IBM should make this enabled by default?