Hi,
that really depends on your custom applications.
1. Are they based on ITS functionality? -> Replace.
2. Just custom programs -> Upgrade and check if they still work
3. BSPs -> Upgrade and check if they still work, consider redoing them using the FPM framework that is used in SRM7
Do a good check on BADI's that are obsolete now, mostly related to the ITS technology (BBP_CUF_BADI_2 and so on), or may work a bit differently (BBP_DOC_CHANGE_BADI - for performance reasons).
Most custom functionality will survive an upgrade. However, an upgrade is a great opportunity to cut out some customer applications and revert back to standard.
Regards,
Robin