That is my question. Personally I think JA 2 (with 1.13, anyway) is one of the best games ever!

I'm a huge fan of Commandos but hardly played the JA games so far (although I bought them from GoG).
I'd say they are quite different since JA is turn-based and Commandos is real-time.
Also you can't choose the people available in a mission and outfit them like in JA.
However both games share the fact that you have to be really concentrated to win them.
At least Commandos is unforgiving (haven't played enough JA to compare).
Usually detection means loading a save game though not always. All the more it's satisfying once you finally pulled a daring maneuvre off.
Commandos is like a game of "mikado". You remove piece by piece (soldier by soldier) until the map is cleared. If you go in guns blazing you will eat dirt in seconds.
Sadly they made Commandos 2 and 3 more approachable and you can do some shooting there but Commandos + addon will punish you brutally for using guns (apart from the sniper rifle and at end of missions).

Apart from the isometric viewpoint, JA2 and Commandos have very little in common. JA is a tactical squad-based wargame and Commandos is essentially a puzzle game which just so happens to take place in a war-like setting. Whereas JA almost exclusively revolves around various combat scenarios, Commandos is all about avoiding combat (and even detection, as intruder points out) and coming up with a smart plan for getting the job done as silently and painlessly as possible.

Commandos:
- max. 6 characters, but mostly less
- 1 mission at a time
- can pick up and use items, but cannot combine or alter them (with exception of sleeping pills with meat or wine)
- no character improvements / no RPG elements
- no 'personal' character
- linear
- no resource management
- classes instead of character stats
- no mods as far as I know (haven't googled)
Jagged Alliance 2:
- max. 18 characters (by memory)
- 1 main mission with a lot of side quests
- can pick up and combine or alter items
- characters get better of time / RPG elements
- 1 or more (1.13) 'personal' aka IMP characters
- none linear, choose your own path to the queen's end
- in the beginning your amount of cash and ammo can be an issue
- no classes but stats which determine a characters abilities and weaknesses
- lots of mods
It's personal I guess, but with JA(2) you grow attached to your characters.
That's not something I had with Commandos.
I agree with you that JA2 is 1 of the best games ever.
Both with and without the 1.13 mod.

After reading that and looking at screenies, I'm guessing the game is similar to [url=http://en.wikipedia.org/wiki/Desperados:_Wanted_Dead_or_Alive]Desperado's.[/url]
Which I thought was pretty good, still have it somewhere :)
Might get this later on.

You're right about that, the basic gameplay is almost exactly the same in Desperados and there is little doubt that they were heavily inspired by Commandos. As said above, it's more of a puzzle game than a tactical squad game like JA2.

Bump for a gameplay question:
Can you pause Commandos while issuing orders to your units?
I play gog's on my netbook and really can't rush and make precise mouse clicks rapidly on it.

Well.. NO, to master Commandos is to master the keyboard shorcuts, the game is impossible to play if you dont use your keyboard as well as your mouse.

That's not always true. There are some maps where you can just hide around a corner with all your men, select them all and start shooting. All soldiers across half the map will blindly run into your line of fire. I usually tried it out of desperation if I had no other choice and it did work at times.
Not good fun though, gets boring pretty quickly and I would have never imagined that there could be 50+ soldiers in one small tent. But if you have the time and dedication, you can clear the map sometimes. :)
!!!SPOILERS!!!
My favourite moment in the whole game was the map with the zoo, not sure if it's expansion or not, played it a long time ago. I got the zoo attendant uniform with the spy and opened the ostrich cage. They ran away, and almost all soldiers ran after them, shooting. I could just walk in to the objective and all that was left was the prisoner to be saved and an execution squad of 3-5 soldiers, all facing the prisoner, couldn't see each other. That was fun killing them one by one.

The Commandos series isn't the same kind of games like Jagged Alliance 2.
Commandos games have more in common with the Desperados games and Robin Hood - Legend of the Sherwood.
But if it's games like Jagged Alliance 2 that you are looking for then you could check out the old Fallout games. They have a similar combatsystem which means when fighting occur the game pauses and you will have time to think about what to do with your precious actionpoints.
Silent Storm and it's expansion Silent Storm Sentinels are also games that are similar to Jagged Alliance 2. However these games have 3D graphics and are placed in the setting of world war 2.
You also have the first Jagged Alliance game that you could play if you liked the second game. Or the expansion to Jagged Alliance 2 called Unfinished Business.There are also a lot of usermade/homemade or whatever it's called modifications made by fans of the game Jagged Alliance 2.
Urban Chaos is one example of an excellent modification to the game! ;)

Combat is part of the Fallout games, but not a major part.
Fallout Tactics is the only game in the Fallout series that's an alternative to JA2.
Another JA2 simular game is 'Hired Guns: The Jagged Edge'.
It was designed to be JA3, but GFI lost the rights to use the JA series.
It scored around 60% in most reviews.

I once played the demo of Silent Storm. Since I liked JA2 I think I might like it. Is it any good? and is there a place where I could get it? Couldn't find it anywhere.

Commandos and JA2 have a few things in common: they belong to the more difficult type of games and need a strategic attitude. However, in gameplay they differ: Commandos is fully real time where you need catch the rythm of waiting and taking action. Most important similarity is that they are both fantastic games!

Commandos is more related to Thief series than JA2.