In the good ol' days of 1st Edition, a mage was worthless for the first few levels, and clerics were good for only a few heals per day. Now we find ourselves in an era of highly effective low-level mages and at-will healing. How can a GM neutralize this situation? Pressure your spellcasters to use up their prepared spells, and keep the action frequent and dangerous.
My last two characters were a druid and a cleric, and I recall constantly yearning for a good breaking point, so the party could find some rest. This was frustrating enough for me to be challenging, without spoiling the fun of playing. It also encouraged me to manage my daily preparations very carefully.
Our GM was clever in anticipating what spells and other effects would likely be in our arsenal, and design encounters accordingly. For example, if a character frequently relied upon energy attacks, the GM would introduce a monster that was immune.
You have to do this carefully, however, or you may appear spiteful or malicious. When encounters routinely demand that the PCs abandon their favorite methods and resources, they will only resent you. Give them just enough of a challenge to skirt total fatigue and spell slot depletion at the end of each day, however, and your game can be appropriately tough.