[hexaae]

Unfortunately there is no rule for WHDLoad games under WUAE: it's generally good to disable JIT-caches but some games may require 'immediate_blits false/true' etc...
I use in S:WhdLoad_cleanup (will be executed when a game exits, no need* to specify for each one ExecuteCleanup=...):

C:uae-configuration immediate_blits true cachesize 8192 cpu_speed max comp_trustbyte direct comp_trustword direct comp_trustlong direct

or that from Mad-Matt is equally very good.

In S:WHDLoad_startup:

C:uae-configuration cachesize 0

as a general rule... but as I said above some games require a proper ExecuteStartup=... (specifying this tooltype the S:WHDLoad_startup will be ignored) where I enable caches for slow games, immediate blitter off, or I use WUAE's option 'finegrain_cpu_speed xxxx', 'cpu_speed real' etc...

*obviously you have to edit S:WHLoad.prefs:
...
ExecuteStartup=S:WHDLoad_start ;command to execute on WHDLoad startup
ExecuteCleanup=S:WHDLoad_cleanup ;command to execute on WHDLoad exit
...