I'll begin with "sharpshooters" as I mentioned them in a particular strategy above. This card should be saved until you have inflicted damage on your opponent. Only then do you try to shoot the general. This forces your opponent to make the morale rolls without that help and before they can replenish the position with another general.
"Uniform Confusion" is a key card that can produce disatrous consequences if used correctly. The best time to use this card is when your opponent is attacking with a high CV unit in a critical situation. A good precaution against this card is to fire with your lowest CV value cards first. This allows them to inflict damage before your opponent can utilize a "UC" card and force you to shoot yourself. Another thing to consider in playing this card is using it at the beginning of an attack, especially if there are only two cards, a 3 and a 4. Instead of taking the damage from the 3 and then hoping that by "UC"'ing the 4 you can get one or both of them, it might be a good idea to "UC" the 3 first. If you get lucky, you might avoid getting hit at all.
"Rally" is one of the best cards to have - it's kind of like an ace in the hole. Judicious use of this card can save an attack from crumbling away. Avoid the temptation to save it until the bitter end. Keeping one card alive when you only have two doesn't really help you - it just prolongs the agony. Use it in a key situation that gives you an advantage. One example might be an attack where you have a 4, 3, 3, 2. You have suffered hits on the 2 and the 3. Depending on the situation, it might be advantageous to ensure that the 3 survives, as it will provide a lot of CV to attack. Look at it this way - a victorious battle in the middle of the war will generally have much more impact than one at the end. Unless you are incredibly evenly matched, by the end it's often just a matter of when and how the winning player is going to finish things off, not if.
"Color Guard" is just like a 1/1 general with the added advantage that it cannot be shot by a sharpshooter. This card is best used in concert with a general to provide great morale assistance. If you are planning an attack and have a "Color Guard", that is where it belongs.
"Double Canister" allows your artillery to double its CV for one shot(short range only). If you have this card and have at least one 3 artillery, it might be OK to have a position that consists entirely of artillery, especially if the 3 artillery is an F3 at close range. Any attack on that position, especially if it is a hill, would amount to suicide as the attackers would likely take at least 4 or 5 hits, depending on the makeup of the other artillery in the position. Other that this particular situation, save the double-canister for when you are attacked with a superior force. Again, unless you are quite evenly matched, don't wait until the end to use this potent weapon. If you sense that you are behind, blast away if you get the chance. It may give you the opportunity to even things out a bit. An interesting anomaly - the south's version of this card does not include the caveat "before terrain modification". Thus the south can turn a 1 artillery into a 4 by placing it on a hill and using this card. I'm not sure if this is a mistake or just another little bonus for the south. As it doesn't really come into play that often, I'm willing to let it ride.
"Forced March" allows your infantry to make two moves during the movement phase. This card is especially useful when making quick assaults on unguarded positions. If your opponent has suffered a large number of hits in a position from a lucky artillery barrage, it may be an ideal time to shoot the general, march the infantry that was guarding the artillery position forward, and fortify this attack on the weakend position with a forced march of a 3 infantry from the reserve and a 2 or 3 cavalry up from the reserve as well. If possible you can also attempt to hit with a flank attack too. This shows the value of a strong reserve. It gives you options.
"Outflank" allows a guaranteed outflank by one infantry unit. Again, this card is best played in concert with a coordinated attack. The best thing about outflanking is the ability to immediately inflict an attack. Thus, holding a 3 or 4 infantry in your reserve along with the "outflank" card is a very potent weapon. Attack normally with a one unit artillery barrage, send the three infantry/cavalry forward, and outflank with the reserve card. You have the opportunity to inflict damage with both the artillery and the immediate flank attack.
"Rebel Yell" (south only) reduces the north's morale rolls in one melee phase by one. Use of this card is obvious. Get in a good melee situation and use it.
"Railroad cards" (south only) allow the south to replenish their reserve by two or three extra cards. The strategy for these cards is easy - if you have them use them immediately. The three card disadvantage built in to the game can be quickly turned around if the player has one or more of these cards.
"Cover" (south only) is like a 1/1 general only better because not only can it not be shot by a sharpshooter, it cannot be hit at all. I'm a little unclear as to the best use of this card as it seems rather disingenuous that units could carry "cover" around with them. I'm more inclined to treat this as a card that is placed in a position during the game and stays there throughout. Kind of like a unique terrain card that can be played in the middle of the game.
Various "Ford" cards allow two cards to cross streams at once. These cards are best used in combination with a flank assault. An interesting way to utilize these cards is to place strong artillery across a stream and blast away. Often times positions behind streams will be guarded less heavily as the potential for attack is limited. When the position is severely hit, place the "Ford" card and attack with two infantry, and attempt a flank (or use an "outflank" card) as well.
When to Attack and How
Breakdown of "Special" Cards (this page)
Strategies for Each Side