I'm using OSX Yosemite and I hate how windows maximization works… previously (with Mountain Lion) I was using RightZoom, in order to always maximize windows as it should be (using the whole space). I discovered that by clicking on the green button with ALT + SHIFT the maximization is applied as I like, BUT is very annoying… so I created a shortcut (CMD+SHIFT+M) by going to preferences > shortcuts > app shortcuts > clicking on "+" and creating a shortcut named "Zoom"… it works great for all the applications but not for the Java ones (or at least it does not work for Intellij Idea and PyCharm)… so… are app shortcuts available only for native Cocoa applications? Is there another way for a fast and simple maximization? (I was thinking about some kind of "defaults write blahblah", but I didn't find anything)
MacOS – Yosemite maximization shortcut and Java applications
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I use Eclipse (64 Bits) latest Indigo version on Lion and I don't have those crashes.
Your Crashlog comes from a Exception Type: EXC_BAD_ACCESS (SIGSEGV) which is usually:
A bug in the code (failure to release/retain/etc.) when coding in obj-c (very common).
A Memory problem (RAM) (hardware).
Given that Eclipse is written in Java (which has Garbage Collection and therefore doesn't suffer from EXC_BAD_ACCESS, as far as I know), I'd say you check your RAM, you might be having a hardware problem that manifests when "memory intensive" (to put it nicely) programs execute.
Welcome to OS X. It can be a great aid to your workflow, and make you more productive. You should be able to adjust pretty quickly after the initial learning curve. Please be advised that there are some small things you'll have to change in your workflow, as OS X is after all a completely different OS. But over time, you'll grow to enjoy it. I'll address your specific concerns.
Dock Behaviour
The Dock has several sections. Assuming you kept your dock on the bottom, the left side contains pinned and currently running apps. This is actually similar to Unity. You can enable a "dot" under running applications by right-clicking an empty space in the Dock and clicking Dock Preferences from the context menu, and selecting Show indicator lights for open applications.
After the divider, which can be clicked and dragged to resize the dock, there are your stacks. Stacks are previews to commonly-accessed folders, and you can drag any folder into this spot. You can preview the contents of stacks in several ways, right-click it to view the stack's options.
To the right of the stacks are the minimised windows or documents. OS X typically dedicates windows to documents, so the terms (especially in the old days) were considered pretty interchangeable.
Window Management
This was one of the biggest pain points when I switched, and now I really enjoy it.
Viewing Application Windows
You can quickly switch between open windows of the same app by pressing Cmd+`.
As you Cmd + Tab, you notice that you're tabbing through apps and not their individual windows. Note that you can activate an app (i.e. un-minimise or un-hide windows by holding down alt (option in the US).
If you want to see what windows an application has, you can either:
- Press the Down arrow while the Cmd + Tab selector box is over the app.
- Right-click the app's dock icon and select "Show All Windows".
- If you are in the app, swipe three or four fingers down on your trackpad (configured by click the Apple on the top left, opening System Preferences, opening Trackpad, navigating to the More Gestures tab, and selecting to activate App Exposé with three or four fingers.).
- Swipe three or four fingers down on its dock icon.
Any of those options (there might be more) will take you to App Exposé, this will show all the open windows in the center of the screen, and any minimised or hidden windows as thumbnails.
Switching to a minimised window in a different workspaces
This behaviour is app-dependent. Using a Finder window, the behaviour is as you wish. i.e. the window un-minimises itself, and the workspace is switched. Make sure to click the minimised window and not the app icon.
You might want to make certain apps available on all your workspaces. To do this, right-click the app's dock icon, and select its behaviour under the Options > Assign To section. The app needs to support this feature.
Moving and Resizing
Windows can be moved using only the chrome (the grey area above the app's actual content). Most of the chrome is on the top of the window, but certain apps such as Finder have bottom chrome that can be used to move the window around.
OS X does not recognise right-click drags. It just doesn't. The only real way to resize windows is by dragging from any edge using the left mouse button.
Using BetterTouchTool
If you want, you can download the excellent BetterTouchTool. Under Preferences, Advanced, Action Settings, Window Moving & Resizing, you can choose to move the window under the mouse by simply holding down a key (e.g. the alt (opt) key.
You can use BTT to change certain behaviours to just the way you want them. It's extremely powerful. You can also assign custom gestures to do almost anything, in any app (or globally).
BetterTouchTool's advanced settings.
Maximising and Zooming
OS X does not use the green "+" button 
to represent "maximise". That's the "zoom" button. The idea is that the app expands itself to occupy as much space as it needs. Unfortunately, the behaviour is extremely inconsistent, especially with third party apps.
More and more apps are beginning to support the FullScreen mode, which was a feature introduced in OS X 10.7 (Lion) 
. This button, if an app has it, will dedicate an entire space to the application. It will be accessible from Mission Control.
I'll give you two options, both involving third-party apps:
BetterTouchTool has an option to enable Windows-style snapping. So when you drag a window to the top of the screen, it will expand to fill the screen.
Another option is to use RightZoom, which claims to change the functionality of the green zoom button to mimic a maximise button. It's free, but I haven't yet tried it.
Shortcuts
You can create a ton of shortcuts in OS X, even to specific menu-items from System Preferences. I'll address your specific concerns here.
Middle click to open and close tabs
I long ago solved this with BetterTouchTool. All you need to do is assign a shortcut like below, and it will be mapped to a three-finger click on your touchpad. You can choose anything else (e.g. three-finger tap if you prefer).
Middle click allow you to open a link in a new tab.
Safari does not support the closing of tabs using middle-click. You either need to click the little "x" that appears over the tab, or press Cmd+W.
Google Chrome supports middle click for both closing tabs.
Global Shortcuts
BetterTouchTool can make quick work of assigning some global shortcuts. I don't think you'll be able to replicate the Ctrl + Alt + B (opens a text box, then executes the command in a terminal).
Cmd + M will minimise a window, no need for BTT for this.
Etc
Apologies, but I can't answer your MOSH question
Alt-2 in Terminal
On my laptop, Alt + 2 produces the euro symbol, so it's keyboard-dependent. If you want the "@" symbol, it's normally found by pressing Shift + 2.
SFTP
I normally use CyberDuck for all my FTP needs. However, a quick web search turned up this: How to mount SFTP shares in Lion.
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Best Answer
It's not strictly speaking about Cocoa apps vs Java apps.
What you're doing when you create a shortcut like that is assigning a keyboard shortcut to existing menu items. So if the application has a "Zoom" menu item, your keyboard shortcut will activate it.
If you have a window open that doesn't have a Zoom menu item, or where the Zoom menu item is disabled, your shortcut won't work.
Your shortcut will work in Eclipse for example, even though it's a Java application, because it provides the Zoom action.
So there won't be a system-wide way to assign a shortcut to this action without using third-party software - either the application provides the Zoom action or it doesn't. It might be worth filing feature requests with the application developers, as it's standard in OS X applications to provide this menu item.