|U| The Uncommon Blue Deck |U|
Blue has traditionally been weak in commons but strong in uncommons. Here's a deck made of relatively inexpensive uncommons and commons...the "dreaded" permissions deck.

4 Counterspell
The essence of this deck. Two land...any spell. Far better than Spell Blast and a must-have for any straight blue deck. Thankfully now common.
4 Dissipate
Just another Counterspell-wannabe. Removal from game is only a small (but nice) bonus.
4 Binding Grasp
Just a Control Magic wannabe, but at least you can steal Nightmares (use it to hold off those dangerous Ornithopters).
4 Boomerang
A very versatile reprinted common. Save your own creatures before they get Plowshared, utterly ruin Howls from Beyond and Berserk, make your opponent pay for putting too many enchantments on her Rabid Wombat, and get rid of some unwanted Meekstone, Maze, or Forcefield for a turn so you can pull off the killing blow. In addition, play it after your opponent's discard phase on some nasty permanent you weren't able to counter before, so you can have a second chance to counter it the next time around with all your mana untapped.
4 Steal Artifact
Although blue has few ways of destroying artifacts, stealing them is often even better. Sideboard out for creatures against non-artifact decks.

4 Air Elemental
Has none of the special abilities of either Serras of Sengirs, but much easier to get, and still able to take them both on in aerial combat.
4 Phantom Monster
A relatively fast medium sized hitter. Not quite as efficient as Whelps but good nonetheless. Underestimated because it is weaker than many heavy hitters, but able to end the game surprisingly quickly if your opponent can't stop it.
3 Tims
A little direct damage can go a long way, but don't rely too heavily on them because of Holy Lights, Pyroclasms, Fireballs, etc. Useful for stopping Orders, Assassins, Ali from Cairo, and much more. If your opponent has no tim-able creatures on the board, don't tim her on your turn...wait patiently to tim her just before your untap phase. Who knows when a Ball Lightning might come roaring down your path? Need to get rid of that annoying Sammy? Tim it at the end of your opponent's turn -- Sammy heals himself -- then tim it again after you untap.
3 Sea Scryer
Add some much needed speed to a slow deck and some protection against land destruction.
3 Wall of Air or 3 Flood
Walls are generally underestimated, but a flying wall that can do damage as well is surprisingly useful for stopping weenie decks. With just 3 mana, you can stop creatures as big as Serras and start dwiddling down the hoards of attacking weenies as well. And good old flood is highly useful against ground-based hammer decks.

19 Island and 4 Svyelunite Temple
Even though the deck is monochromatic, a decent amount of land is needed to power spell counters and the medium to large creatures. Temples are ideal for counterspelling when you need the rest of your land to cast something else.

|U| Sideboard |U|

The deck is already fairly versatile by itself. You may want to finish out your sideboard so that you will always have 4 each of Tims, Walls, Scryers, and Floods at your disposal. One of the weaknesses of this deck is a good weenie deck. That is why a varied weenie defense is helpful. Tims can stop banders, and Walls survive Holy Light.

Against enchantments, this deck may have real problems. Feedback and Power Leak just are not useful enough; even Enchantment Alteration is probably better. But for non-targeted enchantments, you'll just have to either counter or boomerang them. CoPs are generally not a problem. Even if someone does have CoP: Blues in her sideboard, you may still be able control her creatures.

3 or 4 Energy Flux
About the only cards this sideboard really needs. Very useful against Mox or Winter Orb/Vise decks.
4 Force of Will
For those decks that just like to sit around doing nothing, while rendering most things useless. Prove that they'll need more than just a lock to keep a good mage down.

|U| Deck Notes |U|

Spell counter decks are centered around jockeying for position. If you are already ahead (that is, if your creatures are doing more damage than your opponent's creatures) and hold spell counters, then do nothing. Just keep your mana untapped so you can counter any move by your opponent to get ahead, while slowly whittling her away with your slight advantage, even if it is only a Tim. The key is to remain in control of the game. Don't go for the quick kill by controlling her White Knight if you already have a wall up...who knows if her next card will be a Djinn or not.

If you suspect that your opponent has sideboarded Tsunamis against you, spells counters don't have to be your only defense. If you already have enough mana to cast whatever is in your hand, you no longer have to play more land. Just keep it in your hand in case Armageddon hits, or if a Hymn to Tourach comes your way.

|U| Improvements |U|

Other than switching to blue/white, playing with Serras, Plowshares, and Disenchants, there aren't too many more uncommons an all-blue deck really needs.

Uncommon improvements:

3 or 4 Fellwar Stone
Mainly a sideboard card, although they can also speed up your creature casting ability. Provide some protection against land destruction decks. One of their most useful features is that they allow you to regenerate that controlled Wisp, steal artifacts with stolen Bandits, and pump that controlled Order.
2 or 3 Mind Bend
Also a sideboard card, in case your opponent is working on some nasty combo that's just asking to get screwed.

Retired cards:

4 Control Magic
Almost like playing two cards with one: not only is your opponent no longer able to use her creature, but you get a creature of your own. This card is often responsible for incredible come-backs.
3 Ghost Ship or 3 Giant Tortoise
Two reprinted (and then unprinted) cards useful in different situations. If your opponent plays with large creatures, the ships become very useful in an all-blue deck. On the other hand, against weenies, a tortoise can stop Savannah Lions cold with very little mana...and it can even survive Lightning. Good sideboard cards to trade with one another between duels.