Wow, I'm surprized after all this time that no one has posted a strategy article for Commands and Colors Ancients. Allow me to go first. I hope to post ideas in small chunks so the thread responses can be more focused on the topic in the title.

1) Maintain your line.
Lone units and units on the end of a line are more susceptible to retreat flags. Units with 2 supporting units can ignore one flag. Lone units and end units are more susceptible to having their rear retreat hexes blocked which can be destructive in the event of a retreat.

2) Strike first.
Since combat is not simultaneous, striking first gives you a chance of wiping out or retreating a unit before they battle back.

3) Bring the battle to your enemy.
Since units pinned to the back of the board are susceptible to blocked retreats, it pays to bring your line to the enemy to give yourself more room for retreat. This is especially true for light cavalry and other units with many retreat hexes.

4) Put leaders in the middle of things.
Leaders give a combat bonus to adjacent units causing helmets to hit. They also help prevent retreats. There are also many cards which order the leader and adjacent units. So don't let leaders sit alone.

5) Manage cards.
There are many tips for this category. I prefer to safe the "First Strike" for late in the game when the enemy is about to score the last victory banner. When possible, I like to save cards for repeated pounding in one zone - this helps you mop up those 1 block units that might otherwise get away.

6) Battle elephants with light troops. Hit them early.
Since elephants battle back with dice equal to the attack, you want to hit the elephants with the 2 dice troops. Also, when possible, hit elephants with missile units so they can't battle back. Also, hit them early to cause rampage damage to nearby friends.

Well, there are a few starters. I welcome folks to add to the list.

Well, this is sort of an addition to 2) but, when you strike try to cut your opponents line in TWO. Especially if you can isolate units this way and finish them off at your leisure. Bonus for isolateing them without a leader.

Also, though this should be obvious, preferably attack units that aren't supported by an enemy leader (to make their battle back less effective).

Well put. My main opponent could stand to read this.

Other tactics:
- If at all possible retreat weakened units away from the front to give them protection--this is mainly due to the victory conditions rewarding elimination of opponent's units. Especially true with light units.
- Leave a some gaps in your second line to allow potential retreats. If unit has no retreat path each retreat die roll become one (or more) hits! This allows filling in gaps if possible.
- Always be aware of the damage a battling back unit can cause.
- Plan you strategy based on the cards you have in hand. Always if possible play cards for which you can follow up with another card. The most dangerous thing you can do is advance aunit an then not be able to order it lack of a card.
- Also note on left/right cards, if you have seen a large number of left cards, your opponent is likely to have a larger than expected number of right cards--which will activate units against your left flank.
- Get your heaviest units into battle. This is how the game is won.

To expand upon the comments about hand management, it is best to try and construct a strategy that involves several cards if possible. Enough to mount an attack and then follow up and consolidate success or, if the attack fails, to retreat and reorganize.

When you don't have a good selection of cards with which to do this, it's often best to move defensively to strengthen or organize your battle lines. Unsupported attacks that leave your unit's exposed to enemy response are a good way to give up easy banners to your opponent. While you are using cards defensively, you can (hopefully) be picking up cards that can be used together in a coherent plan.

The game also rewards historical use of units. Use light infantry/cavalry to disrupt heavier units with ranged fire and evade if attacked. Then close in with the heavier units at a point where you've created weakness with your light units.

About protecting your flanks, another way to make a flank strong is to put a leader with the end unit. This unit can then ignore at least one flag, just as if it was supported. It also gives that unit and the one adjacent to it the extra punch in combat of counting the Leader hits. That should make that flank look a lot less attractive to your opponent as a point of attack.

Given a selection of fairly equal strength targets for ranged attacks go for the heavier units, as your odds of hitting are equal, but weakening the heavier units is more valuable. Also, choose a unit with a leader over one without. A hit gives you a chance to eliminate the leader.

Finally, try to play more aggressively when you're ahead in banners. Even losses will get you to victory before your opponent.

Light cavalry is very vulnerable and near-useless in CC. Surrounded enemies often beat them up! Infantry units can catch them even when they are positioned to discharge missiles, and they only have three blocks. They are portrayed noticeably less successfully than all the other elements of the game [so we might consider giving them back their crossed swords]. As such you would do well to consider them a potential advantage in banners to the other side. Keep them out of trouble and don't let them within two hexes of anything ferocious.

Medium cavalry is probably the most powerful unit type in the game. It has a movement of three which beats all light infantry to the draw. A battle-back banner [or two] from the survivors of a charge is a gift to these boys, as they can retire from trouble on their opponents turn. Under a leader even a single unit can stuff two enemy units off one card play.

This last also applies to Heavy Cav, once they lumber into action.
Heavy infantry and Medium infantry also lumber, and the penalty for this is missiles poured into them. Warriors charging is all very well but unlike cavalry they sometimes have trouble retiring alive, as after a charge they tend to find themselves first outnumbered and then dead shortly after. So don't let Warriors turn into banners for the enemy. All these units types must be brought into action together as soon as possible [to win], and the real reason for maintaining or reforming one big line is to allow this, by use of Line Commands, with banner support being a useful protection for your investment in movement cards.
As an aside, the most powerful cards are those that allow movement of all mediums or all heavies. There's not much you can do about these cards in most situations. In this case card-counting is perhaps justified.

Most units can be blown away suddenly, so offensive strength should not be mistaken for robustness. If you position a unit where it can be attacked by many enemies you'll probably lose it.

Its amazing how long a single-block Chariot can survive in the front line, ignoring all those crossed sword hits, battling back all the while.

Lights, Bows and Slings are sometimes useful for masking medium and heavy infantry from missile fire, as they move into action. Obviously their best function is to rain missiles on the heaviest units with the fewest blocks.

Leaders are also a banner to the other side, and its unfortunate to lose a battle this way. Otherwise it is usually worth moving them into action wherever and whenever possible, to get the extra hits, instead of moving a unit.

Lastly, most strategy is scenario-specific. At Cannae the Roman cavalry must take out the opposing cavalry at the earliest opportunity, despite appearances, and at Ticinus the Carthaginian light cav should be assailed with similar prejudice asap. If you lose at least you know you did the right thing. At Lake Trasimenus the hills nullify the Carthaginian Warriors, whilst the Carthaginian cavalry is in positional trouble from the start.

A few more:

-Move units onto the hexes shared by center and flank. This gives the unit more flexibility as more cards may control it.

-When facing non-missle units, keep missle units at their maximum range. This allows you more shots and the enemy units are forced to close with you.

-Target the blocked unit. If an enemy's retreat path is blocked, target it. Banners are turned into casualties.

-Battle from your strong section. If Player A has strong flanks and Player B has a strong center, Player A should battle from the flanks and Player B should battle from the center. A superior force is often nullified when the commander does not move it into fighting position.