I was looking for the best way to get to the 100% in Saints Row 3, and I must say, with the site of IGN, it’s pretty straight forward.
This is what you should do, divided in 4 golden steps:
1- Complete all missions
2- Complete the activities on the map : http://www.ign.com/wikis/saints-row-the-third/Activities
3- Complete the Saints Book section of the mobile phone: http://www.ign.com/wikis/saints-row-the-third/Saints_Book
4- Upgrade everything you can: http://www.ign.com/wikis/saints-row-the-third/Upgrades
Hope it helps