Regarding MyISAM vs.InnoDB..... I had much higher CPU load and call delay stablishment using InnoDB and I had to switch to MyISAM. Not to mention 3x disk space, which is nowadays not "really" important.
BUT this highly depends on the implementation of your application. If they are not able to react upon transaction failure (innoDB) then you do not gain much using it and you should go for MyISAM.
I would recommend using MyISAM for fast updates (accounting,location,...) and innoDB for more "static" data but i'm just a DB newby and would really appreciate someone with knowledge to correct me!!!!!!
just test it,
samuel.