I've been wondering this as well?
I'm not sure if the traditions are the same through all Orthodox churches, but in our church, we cross ourselves at certain times.
I understand why, when the Trinity is mentioned (at least that was what was explained to me).
But why does almost everyone do it when the Theotokos is mentioned? And as well, most do it during the Creed when the Church is mentioned?
I´ve heard my priest say that every time we cross ourselves it´s either a way of praising and glorifying God through his name, of the Father, Son and Holy Spirit. So when we remember Saints, the Church and all it´s truth in different matters we, by crossing ourselves, are praising God for the work He has done for us to grant salvation, through other people, his Church and many different things.
Or, as the priest mentioned, by the sign of the cross we are given one of the strongest, personal and easiest way to bless ourselves. So when we remember the Holy Theotokos, the church in the creed, Saints, their relics in our prayers and actions towards God, He actually in the process blesses us so as we through the sign of the cross both praise Him for all things and for all His work.
Pray for me and forgive me, the sinner