Typically, you will need to reference:
The "new" DPS indexing algorithm in mosflm
Ingo Steller Robert Bolotovsky and Michael Rossmann (1998) J. Appl. Cryst. 30, 1036-1040.
You should also, separately, reference individual CCP4 programs that Elves run:
crossec, dm, fft, freerflag, overlapmap, postref, rantan, revise, scala, scaleit, truncate, vecref
details on citing these are listed on the CCP4 website.
If Elves run solve, then you should reference it:
Terwilliger, T.C. and J. Berendzen. (1999) "Automated structure solution for MIR and MAD". Acta Crystallographica D55, 849-861.
If Elves run shelx, you should reference it:
If you use denzo to index your first image, you should reference denzo:ref?
Note, if Elves downloaded ccp4 or mosflm for you, then you should be sure to fill out the CCP4 licence form, and send it in to CCP4!