Counterspelling is a completely legitimate and *nasty* approach for a DM to take. It has a potentially huge impact upon your game and keeps things fresh, interesting and changes how battles unfold greatly.
If your players do not attempt counterspells, your NPC's should to add variety and tactical disruption to your encounters to teach them the benefits of doing so.
Situations where Counterspelling assists:
1 - Larger Number of Mooks
I tend to throw large number of foes at my players that are supporting higher level NPCs. There may be 20, 30 or even 50 low level 1 to 4 HD creatures present in addition to the more serious bad guys. This typically is not a terrible challenge to the Players on their own (party level is effectively 8).
But my campaign is the War of the Lance and I like to feature the WAR element in the adventures. This implies armies and lots of bad guys.
When throwing large numbers of relatively weak foes at a party of adventurers, the primary attack of the party to cut through the mooks to get at the serous bad guys will be fireball.
By saving sigfnificant numbers of low power bad guys, you will end up disrupting the party far more effectively than by casting fireball in kind. The greater elements of delay this provides allow you to leverage the more significant power of the larger nasties BBEGs for longer.
2- Critical Spell Disruption (Cherry Picking)
Battles have their own plans and their own rythyms. The old addage that no plan survives contact with the enemy is never more true than when you selectively target spell disruption via counterspelling. If your players are highly tactical and extremely experienced, they will focus a lot of power and planning on your encounters. My groups sure does. CR be damned, my group of players effectively increases the ECL of the party by at least +3 to +5 IMO. They are that good.
Nothing acts to reduce this "extremely experienced players" bonus like dispel magic and selective counterspelling (cherry pick) at opportune moments.