Develop Reference

What do I have to learn or should use in creating a 3D android game?

My thesis is to create an 3D android game. I have installed the 3D softwares like 3DS Max, ZBrush, Blender. I also downloaded Android SDK for Windows and I have Eclipse Juno. But I don't know how to start. Thank you in advance. :)

If you want to write a game, use a game engine.
I would advice against using OpenGL directly if you want to focus
on game mechanics or story. 3D game engines like
Unity or JMonkeyEngine
give you all the tools you need to turn your 3D assets into a game:
Importers for various file formats, a scene graph,
math libraries, and usually tons of example projects that get you
started quickly.
If you want to write a rendering engine, use OpenGL
With OpenGL you can build everything mentioned above yourself: Write
or find importers for your assets, figure out a lighting model, write
a scene graph. If you want to do all that, cool, use OpenGL. But
doing this technical stuff will keep you busy; you will have less time
to make a really great game.

I prefer OpenGL ES for Android. Good performance and easy enough to learn.

It's better to start from basic with opengl and then understand concept of using 3d and then prefer standard tool to use.
I have listed android game engine tool for 2d and 3d. Hope it might help u.
https://stackoverflow.com/questions/17163446/what-is-the-best-2d-game-engine-for-android/17166794#17166794

Start with unity3d which is a game engine, I am not sure but the names that you have posted are used for making 3d models for the game.

Your Thesis? That's pretty broad scope! :)
What I would be looking for, is something with lots of example code (since you say you don't know where to start) and good community involvement (ditto the start thing).
If you only need a single player setting, then I would suggest libGDX as a place that would be a good jumping off platform, as there are lots and lots of step thru tutorials along with lots of example code (and a very up to date wiki on the API), and a pretty good group at helping out with issues.
Since it is open source, you can dig as deep as you want into the inner workings to understand (or be mystified like me) as to how the code is accomplishing whatever task you are looking at. (which might be handy for your thesis)
While it might not be quite as polished as some other commercial 3d development kits, the BadLogic crew has made some very big progress the past few months on the 3d side of the house, along with breaking my JSON code... thanks! :) )

What libraries for interactive 3D model in Android AR app?

I'm asked to do an app with a 3D object mapped on a tag on the camera preview. The user should be able to rotate the 3D object on swipes, and to click on different area of the 3D object.
I'm investigating the different way to do it.
So far the best option I've found seems to be https://developer.vuforia.com/resources/sdk/unity, but I can't find whether it's possible to interact with the 3d model (rotate on swipe, define clickable areas).
Has anyone any experience with that?
I guess I can do it with some OpenGL, but I have no experience with it and it seems quite complex to start off with.
Is there any other library I should consider?

I would use OpenGL and start by the training tutorials on http://developer.android.com/training/graphics/opengl/index.html. Hope this helps! If you follow these tutorials you will be able to do what you want. ive tried unity and it is a really good engine too. and of course you can make an object clickable with unity! maybe using unity would be easier but the documentation on opengl is huge and is not that difficult to implement at least with first steps. hope this helps

The Metaio SDK can do all of that but I am not sure if it automatically provides the area of the model tapped, but you could ask here.

3D waving flag in Android (using cloth simulation)

My goal is to create a waving flag in Android using OpenGL but I don't have any clue on where to start.
Cloth modeling seems to make the neatest effect but I couldn't find any implementation for Android on the web.
I hope that someone would know some tutorials, resources etc. that could help me solve this problem.
If you know easier/other ways to create a decent looking waving flag, let me know. I'm open for everything.
Thanks in advance!

First result on google
http://code.google.com/p/waving-flag-android/

A good tutorial about cloth simulation is from Jesper Mosegaard http://cg.alexandra.dk/2009/06/02/mosegaards-cloth-simulation-coding-tutorial/
The pioneer work on cloth simulation is from Darwin 3D http://www.darwin3d.com/gdm1999.htm#gdm0599
A open source project in Google Code provides a variety of algorithms http://code.google.com/p/opencloth/
All these works are based on C/C++ which is the natural programming language for OpenGL. As you are working on an Android project, you have to rewrite the algorithms in Java. After you figure out the mechanism, you should be fine. Good luck!

Which Framework choosing for 3D animation on Android?

I started to develop an Android application, and I would like to run a 3D animation at launch, showing a car in 3D. It will be my first experience, as a result I would like to know what framework i have to use?. I've heard about min3D but I can't find documentation to guide me in my development from A to Z

Since you asked also about choosing a framework, I want to recommend one more than the min3d. Take a look to Rajawali Framework.
There is big list of Rajawali tutorials here. Also you can download Android project with examples from github.
I'm very impressed with this library!

How to load 3D models with min3D, a tutorial: see this link
you can also see this project it seem it target your same goal sources are also attached, feel free to focus on it and get some benefis. min3d car

How to start with 2D

Ok my question is simple:
How do I start working with 2D graphics on android? Untill now,I found on the how to make almost anything on Android,however with graphics I see is harder.
On the android sdk website,I get some simple codes that don't really help me,and I also searched for a book,guess what,I didn't find one that actually shows you how to make a little game explaining me what does every line of code.
So: How do I start working with 2D graphics? I'm interested because I want to make some games.I would be very happy to find a tutorial for ex. that shows you how to make a little character that just jumps over a box.I know you need an engine and all that stuff,and I would actually want to learn how to make a little engine.

libGDX runs on Android (and a few other platforms) and provides high level 2D graphics features like sprites, fonts, tile maps, particles, etc.
Tutorials here.
A few complete demo games with source code here.

Here's a whole series that seems pretty decent, and starts from the beginning.
Also, the techniques of "generic" 2D programming apply, so general-purpose game engine information is useful as well.

If you are interested in android games(2d), I recommend this book http://www.amazon.com/dp/1430230428/

The following book is very good for learning 2d graphics in Android.
"Android 2D graphics with Canvas API".
http://www.amazon.com/Android-Graphics-Canvas-API-ebook/dp/B00DKIAVK8/ref=sr_1_8?s=books&ie=UTF8&qid=1374420538&sr=1-8&keywords=android+2d
It is not for game developers though.
It teaches how to use graphics primitives and work with different coordinate systems. It also has a chapter on multithreading.
It has many simple examples good for beginners.