The old combat calculator has been replaced by a fancier Java application called the Analyzer that runs on your computer. If you already have the Java Runtime installed, download ALAnalyzer.zip and follow the instructions in the README file. If you don't have the Java Runtime installed, you can download it here.
I am in the process of converting the calculator to Flash so that it will run directly from the browser (and eventually on your Android phone), but it is taking a while due to my other commitments.
The combat analyzer allows you to test the results of a single combat action or analyze the results of thousands of similar combat actions. The image below shows an example of an 8-die Xenophobic attacker in close combat with a 4-die defender that is under the influence of Bad Luck.

To view the results of a combat, select the number of dice icons showing for the attacker and the defender in the number boxes at the top. Below each number box is a panel listing special abilities and conditions. Select the ones that apply by checking the boxes or indicating the number of icons. Indicate in the Combat type box whether the combat is close or ranged, then click the ANALYZE button. The results of the combat are shown in the log.
In addition to analyzing a single fight, you can request an empirical analysis of how a combat would work over the long haul. An empirical analysis will display a graph showing the expected damage: expected damage to the defender is shown in green; expected damage to the attacker is shown in red. The screen shot below shows a graph for the Xenophobic/Bad-Luck fight simulated above.

You view the graph by clicking on the Graph tab.
In this graph, you can see that there is roughly a 20% chance each the defender will take 6 or 7 hits. The attacker has an over 90% chance of escaping undamaged, a less than 10% chance of taking 1 hit, and a very small chance of taking more damage than that. The numbers used to generate the graph are shown in the table.

The Dmg column contains damage amounts (0 hits through 12 hits). The A Hit column shows the percent chance of the attacker taking that amount of damage. The A Kill column shows the percent chance of an attacker with that number of hit points being killed (this is called a cumulative percentage). The D Hit column shows the percent chance of the defender taking the given amoung of damage. The D Kill column shows the percent chance of a defender with that number of hit points being killed. So, for example, in this combat situation the defender has a 19% chance of taking 6 hit points of damage. If the defender has only 6 hit points to being with, it has a 68% chance of being killed.
You can adjust the combat and click ANALYZE again to see what difference a small change makes. The previous graph line will be faded a little and the new graph lines shown on top of it. For example, the graph below shows what happens when the defender is no longer subject to Bad Luck.

Without Bad Luck, the red line shifts a little to the right, indicating that the attacker is at higher risk for damage, and the green line shifts to the left, indicating that the defender will take less damage. You can continue to make changes and plot new graphs to your heart's content, though the old lines will get pretty dim. Below you can see the results of removing Xenophobic from the attacker, which has a much more dramatic effect.

The Analyzer will also analyze how particular units will fare in general combat situations against opponents with differing dice counts. An Attack analysis computes the expected (mean) damage by a fixed attack for varying numbers of opposing defense dice. A Defense analysis computes the expected damage against a fixed defense for varying numbers of opposing attack dice. For example, the graph below shows an attack analysis for an attack with 8 dice.

The green line shows that if there are 0 defense dice, the expected damage is a little over 5. It decreases steadily until we see that against 12 dice the mean damage is only a single hit. Conversely, the red line shows that the damage taken by the attacker will be 0 if there are no defense dice, but it starts to increase rapidly around 6 defense dice. At 8 defense dice, the expected damage is the same in both directions, which makes sense.
The graph below is the converse analysis: how a unit with 4 defense dice will perform against different numbers of attack dice. As always, the red line shows expected damage to the attacker and the green line expected damage to the defender.

As with a combat analysis, the Table tab displays the raw data for an attack or defense analysis. In this case, the first column (Dice) shows the number of opposing dice, the second column (A Dmg) shows the mean damage to the attacker, and the third column (D Dmg) shows the mean damage to the defender.
For a complete description of the analyzer's options, see Calculator Help.