This is how the final score is figured.

[Poopyhead]

Really.
First, these things don't figure in your score:
"I see dead people." The final screen that has what you lost and what he lost is just eye candy. If you bagged 300 conscripts and 30 BT-7s but lost 100 elite Nazi stormtroopers and 10 Tigers, you probably won't be crowing about what looks like a 3-1 kill ratio.
The price of artwork is zero. Even I thought that you got a bonus factor for winning quickly with a few surgically placed karate chops, but you do not. The Hannibal Lectors of the world won this one. If you want more points, then be merciless.

Now, I am absolutely sure that the following does count:
The total points awarded to you for Victory Hexes. Sometimes you get victory points per turn, so you may have to take some notes to keep track of this number.
You get points equal to the total battle damage you inflict. To determine this, go on the final screen to the buttons on the bottom (View Map, Save Score, Player 1, Player 2 and Done). If you were Player 1, then click Player 2's button. As you probably already know, you will see player 2's unit list. Add up the red numbers in the "Dam" column. This sum gets added to your score. (Update: the 1 damage point listed for units that malfunction does not get added to the score. I guess the AI figures that the system will eventually be fixed. Also, minor damage to aircraft does not count. I don't know why.)
You also get a bonus for units that you damaged, but did not destroy (this number will not be in red, you must calculate it yourself if you want to check it!), equal to the total score for that unit if you had destroyed it, times the ratio of the damage done to the whole unit. Mmmmkaay. For example, if I got 3 of the 6 men in A0 (worth 200 points), I would then get half (3/6) of the 200 points for that unit, or 100 points for those 3 men. Again, you must calculate this yourself for each damaged unit, as it does not otherwise show up except in the Victory Score total.
Now comes the hair-splitting. Damage points for vehicles are not easy to figure by any obvious means. I used 2 tanks in the test battle. I destroyed one to set a baseline and did 3 points of damage to the other identical tank. I got 67 points for the destroyed tank and 50 (about 70%)for the damaged tank. I figure that the score is determined as a percentage of crew lost to the entire crew. Also, the value of a unit is the base value you spent to buy it. I had five armored cars with varying experience that changed their listed cost, but I got the same "Dam" points for destroying them.
Another problem is results with fractions. When you figure a score for a damaged unit, everything after a decimal is lost, i.e., 2.9 becomes 2.
Additionally, on rare occasions one side can be awarded points for retreating units off the map. That side gets three times the unit's value and the other side gets half the unit's value. If you get reinforcements, your opponent gets 25% of their value as victory points in addition to any points for damaging or destroying them.
Update: Mosh had a post that a designer may increase the value of a unit by a multiple and I found that page 137 in the manual confirms this. A lost unit may cost you 10-100% more than is shown in the "Dam" column. Whether the designer wishes to tell you that he has done this is something that I cannot confirm, although you can figure this out for yourself if the score looks way off.
So recapping, your score is the total points for victory hexes awarded, plus the sum of the battle damage inflicted, plus a bonus for units damaged, but not destroyed (and any bonuses for retreated units, or reinforcement units, or arranged by a scenario designer).
I swear or affirm that the statement I've made is true to the best of my knowledge, so help me Heaven Six. And you're welcome!

[ILCK]

So in otherwords, run down those fleeing infantry units in the last two turns. [;)]

Question, how do crews figure in? If I destroy a tank and the crew, presumably dies inside in the fireball do I get more, less or same if I force the crew to abandon and then mow them down?

[Poopyhead]

I was working on that when South Park came on (back to back episodes!). I think you get more points for this. Actually, you can make the calculation real simple if you just destroy anything that turns the cursor into a bullseye. That way you don't need Brainiac to figure out where those last few points came from. I was able to determine about 95-100% of my score, and I knew what the computer did for the rest, even if I didn't know exactly what 3 damage points equated to for a vehicle.

[Voriax]

Poopyhead, interesting. However during some tests I did a while ago the game did not award points based on % of unit damaged. for example, when I was shooting at a Sov infantry squad I got 1 point = 1 casualty, no matter how many men I eliminated from my target squad. See this thread: tm.asp?m=618117

Voriax

[Poopyhead]

Interesting. I know that in my test, the Germans lost 7 men, from I think a total of four infantry units. I took the percentage of each of the units damaged (truncating the decimals) and added them up. The sum was 100% correct for my score. If there are gray areas, we should be able to figure them out if enough people test for things like what you point out. I just can't accept that this is beyond solution. I'll do some more testing tonight and see if I can recreate some situations like you describe. I'm also interested in how reinforcement points show up in the Victory Score and if percentage damage that comes out to less than one point gets rounded up (.1 becoming 1).

I'm not an abstract thinker, so I'll see if I can reproduce the ATG/infantry squad problem. Also, it may be as Belisarius mentioned, that the program keeps a running total of incremental damage and then gives you the full value again when the system is finally destroyed. It should be possible to test this. I'll try it out during the South Park marathon this weekend.

Okay, I also got only 12 points (not the listed 23 points in red) for the Sov infantry squad alone, although the "survivors dispersed" before I could annihilate it. However, when I took out the squad and the ATG together, I got the 23 for the squad and the 49 for the ATG and an extra 14 points. This was less than one percent of the total score, though, and it seems that when many units get destroyed, the unknown points don't grow larger as a percentage, but stay small.

[Poopyhead]

The value for a weapon destroyed with its whole crew, or part of its crew or none of its crew (abandoned) is the same. If the crew (or partial crew) bails out, then it is a new unit that can also sustain losses for additional victory points. The new crew unit usually has a low value (6 man unit for 4 points).
Last night I was again able to calculate my final score with great accuracy (I got 103 points in the test score and I had figured up 101). Ordering reinforcements, however, did not work as advertised. The other side got nearly 100% of the reinforcement value. I did not use them in combat and should have lost only 25% of their value, so that is still a gray area. (Update: after repeated tests, I do get 25%) However, the system works. Points for VH's and red "Dam" points will usually give you about 80+% of your score and although figuring the percentage score for damaged units is tedious (you can still just concentrate on destroying everything), it should fill the gap remaining, leaving only a couple of "mystery points" from a score of thousands.

As a further update, damage from malfunctions apparently do not count or minor damage to aircraft. I believe that anomalies with the steel.prf file also change the score for a unit, so it is best to replace this file often. I just make a copy of the initial file with my settings on my desktop and overwrite the old steel.prf with it (which is a steel.dat file in Win XP). That way I don't have to reset my preferences every time.