When I am in Admin->Field Management trying to lookup whether a Marketo field is custom or not, it doesn't seem like there is a way to do this currently but I could be wrong. Even though I was the one who created the custom field, I have a hard time recalling the name the of the custom field unless I documented it in Excel. It would be even harder if another person who did not create the field trying to look up this information.
One idea is to have a different icon for Marketo Custom Field versus System Created Field. There are obviously many other ways to do this such as enhancing the find search box.