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What is the best script language for Unity3D

I am starting with game dev using Unity3d and I can see there's 3 supported languages for creating scripts: C#, unityscript and Boo...
although, coming from a web-design past I am obviously used with javascript, but after few attempts I could notice Unity3d doesn't really have full support to the script language and some elements like new Date().valueOf() and some other statements within methods such as the attribute arguments and many other won't work properly, also it seems my file can't have a wrapper method that envolves all the other methods like:
(function (scope) {
function Start() {
...
}
...
}(this));
and when using something like new Date().valueOf() which is valid in JS I get:
MissingMethodException: Method not found: 'System.DateTime.valueOf'. Boo.Lang.Runtime.DynamicDispatching.MethodDispatcherFactory.ProduceExtensionDispatcher ()
So perhaps the compiler turns that initial 'unityscript' code into Boo language? so perhaps Boo is the right 'native' choice and maybe unityscript itself isn't the best way to go when developing unity3d apps?
I was thinking on a language that has full support to all known native classes and methods which will work without problem?
Sorry for any errors mentioned above and please let me know what you think.

Unity doesn't use 'real' Javascript per se. See:
http://forum.unity3d.com/threads/1117-Javascript-Version
UnityScript is based on javascript 2.0. There are a few things missing (switch statements, etc.), but they get half the speed of C++, which is way faster than Mozilla.
Once you get used to it, developing in 'JS' for unity is very very fast and flexible...but of course, if you're going to develop native components, or interface to anything in C, you'll need to use C# (in the end, C# is not difficult to learn).

If you want to be a developer in Unity and build a career on it, learn C# and use it - don't waste your time with UnityScript. You can use C# outside of Unity for programming. If your main career is already web development (or will be), then continue using javascript because ultimately C# and UnityScript have the same functionality but C# is much more widely used for programing games and applications.
The majority of the assets on the store that I have used are C# or offer both JS and C#. Mixing between the languages creates serious dependency problems because in order to use a class in either language it has to already have been processed by the Unity script loading order. To use a Javascript defined class in C#, that script file must have been processed prior to the C# script file. If the javscript class then later needs something from the C# class, you would have to find ways around it because its simply no longer possible from the javascript file. Unity has ways to define the script order.
I thought that I would warn you about mixing C# with UnityScript because if you don't focus on one or the other, you will run into this problem. Ultimately, C# is the middle ground between ambiguous languages like VB and JavaScript, and pedantic languages like C++ (I have a C/C++ background of about 10 years).
Your title "What is the best xxx" leads to opinionated answers, but I am trying to give the best advice possible without being subjective. C# will allow you to continue, even if Unity were to go away a year from now. UnityScript/JavaScript would only allow you to move into being a web developer. A C# developer can easily move into UnityScript/JavaScript, but the reverse is much harder (not impossible, just more difficult).

You should use c#. It is popular, mature, native to .NET. c# is what big teams use. Learning c# will be useful in the future. JS in Unity3D is not real JS as already mentioned and nobody heard of Boo.

JS is the most popular language for use with Unity. But the language is implemented in Mono, and so any restrictions in that implementation are going to affect Unity scripts too.
I don't know how the Mono implementation of JS works, but judging from the error message, it uses datatypes initially defined for Boo, at least. However, that doesn't mean that JS is "turned into Boo". Both are compiled into the same bytecode, which is JIT'ed and run by the Mono runtime. So neither language is "more native" than the other.

Checkout advantages and disadvantages of using c# and Java script from here.
C# is little bit faster than JavaScript and you get extra features provided by C#. You can get peoples opinion from here.
Developing with c# has advantage of Visual Studio 2010. It provides better code completion feature than Mono develop.
In JavaScript only, variables can have an unspecified type. This only occurs if you do not assign a value while declaring the variable.
Performance is slower with dynamically typed variables, and you can run into casting problems. Iif this is a concern, use #pragma strict.

Multilanguage development

I would like to develop an application with two languages.
Actually, the goal is to generate two differents application, one with a language (Java), the other on in another language (C#).
I would like to use makefiles to help me generate one application or the other one, thanks to targets definition.
I don't know where to begin.
Have you ever try to develop like this ?
Is it possible to use one makefile to call java compiler or c# compiler using different targets ?
Thanks in advance for your help.

Sure, you can use a make file to compile (and link) source files for different languages. There's no limitation. All you need is a compiler (linker) that can be called by a shell / from a command line.
Alternatives: ant can do both Java and C#. If you don't need to build both applications with a single build file, you still can use separate files and write a batch/shell script to call both builders.

Yes it is possible to override a Makefile variable to point to either javac or the .NET compiler.
You will, however, most likely not benefit from this as it is very hard to write a program that is valid in both languages.
You may want to look into http://www.ikvm.net/ which provides a Java emulation environment under .NET, so if you have a Java program it can run under .NET.

There is also the Fantom project, which claims to do that, but I have strong doubts regarding cross-platform support (how can you abstract all side-effects of all APIs?).
But I don't know the project, maybe they do a fine job.
http://fantom.org/

my idea is pretty dumb but i guess you could try this:
step 1: make a bat file
step 2: make the 2 script files
step 3: make it so it executes both of them!
#echo off
start yourfile.script
start yourfile.script
this idea is gonna fail

C# scripting from C++?

Is there any C# interpreter that can be used inside C++ and yet still allow .Net access?
I want to use C# scripts for games and I'm not sure how to proceed with that.

You can write a simple class in C#, let's call it ScriptRunner that would take your C# code as input, compile it at runtime to produce a new assembly in memory, then it will use Reflection to load a specific Type from this new assembly, and will run some method with an expected name.
Then, use COM Interop (for example) to create a ScriptRunner .NET object from your C++ native application, and you'll be able to use it to run scripts.
Start with:
var myProvider = Microsoft.CSharp.CSharpCodeProvider.CreateProvider();
var myCompiler = myProvider.CreateCompiler();
and it's really easy to continue on your own by using IntelliSense to see what's on the ICodeCompiler interface.
If you've got some specific questions about this approach please ask.

C# is not an interpreted language, it is a compiled language.
You can write C# scripts, but why not use Python or Ruby or Lua or some other true-blue scripting language?
I feel somewhat dirty mentioning this, but it looks like there is an ECMA compliant C# scripting engine.

I believe C# is a compiled language only. Your best bet would be to call the csharp compiler (csc.exe) and load the assembly dynamically.

YOu can have .net dlls and use them in your C++ code.

Is it C++ or C++/CLI? If it's the "normal" C++ I don't think it will be possible to use C# as it is a compiled language and a managed one, your best bet would be to use the managed version of C++ and compile the C# code, then load it.

I've never tried to do that but I think C# is definitely not a suitable language for scripting, for your purpose Lua or Python (for example) are certainly better...

I assume you want to use C++ for DirectX/OpenGL support and then want to load in the entire .Net Framework on top of that to support scripting? That would be a very heavy footprint if it were possible. Since C# is compiled into bytecode (just like Java), you would have to precompile your scripts.
Your best best is to to use an opensource scripting language (php, lua, etc).

Can I execute a single C# statement as a script?

I have seen online how C# allows you to compile code on the fly and I think that is a really awesome thing. I need to use this functionality for my project. But here is the problem. I'm not trying to compile a whole function or new program dynamically. I just need to call a single statement to create or delete stuff on the fly.
Is there a way C# can compile and/or run a single code statement and allow that statement to act on variables and objects in the current program's scope?
Thanks

You could compile C# using Microsoft.CSharp.CSharpCodeProvider, but that gets really complicated if you want to do it correctly, since you need to load your code in a separate App Domain to prevent memory leaks.
I'd suggest using IronPython or some other DLR language: http://www.codeplex.com/wikipage?ProjectName=IronPython
Some sample here, not sure how up-to-date it is but the idea's pretty much the same: http://www.voidspace.org.uk/ironpython/dlr_hosting.shtml

To give you an alternative rather than using C# as a scripting language, have a look at Conscript [1].
Conscript is a compiled scripting language for .NET.
[1]: http://www.codeproject.com/KB/cs/Conscript.aspx

"I just need to call a single statement to create or delete stuff on the fly." Statements like these make me shudder down to my bones. What are you trying to accomplish here, really? You want to have your user write C# statements and have your program execute them within its AppDomain? Not only is this an immense security risk, it is also a terrible user experience.
Furthermore, C# is not a scripting language. If you try to shoehorn it into being one, You're Gonna Have A Bad Time (TM).

You can, while using the debugger. At a breakpoint, just type some code into the Immediate Window in VS, and viola.
One of the best debugging features there are!

Scripting static languages comes trade-offs. There are scope and security concerns to consider, but they can be controlled.
If you're looking to execute static code (i.e. C#) from within a managed run time, I'd recommend starting with Mono. The Mono team has made strides creating a safe environment to compile JIT code into native code at run time.
Start with their official post on the subject.

It depends on what you are trying to do ... if you are looking to use it as an embedded scripting language within another application, then my answer doesn't apply, but if you just want to execute random C# statements (or programs if you like) and save them as scripts, LinqPad is awesome for that.

Generate and parse Python code from C# application

I need to generate Python code to be more specific IronPyton. I also need to be able to parse the code and to load it into AST. I just started looking at some tools. I played with "Oslo" and made a decision that it's not the right tool for me. I just looked very briefly at Coco/R and it looks promising.
Does anyone use Coco/R?
If you did what's your experience with the tool
Can you recommend some other tool?

The IronPython implementation itself includes a parser and an AST representation of Python programs which can be walked with a PythonWalker.

Not really my area of expertise but you might want to try ANTLR 4. It has support for generating Python 2 and Python 3.

I think you should look at the Dynamic Language Runtime. This will be a standard part of some later version of .Net and C# (.Net 4 from memory).
I've used it to compile and execute Python code generated at runtime, but I haven't played with all the AST stuff yet.