A few things they've done:
1. They've created baggage fees for checking bags: That accounts for +$50
2. The YQ/Fuel charge: You're subject on their pricing of fuel
3. Seat Charges: If you want to reserve a seat before checking, some airlines charge for this (Namely AA)
4. Fees for printing a BP (Ryan Air), checking in at the airport (Ryan Air again), Carry on luggage (Spirit), etc
5. Charging for alcohol on long haul flights (I'm rather fine with it.. but it used to be customary)
6. Charging for food on long haul flights. (I'm looking at you US Airways CLT-AUR)