Recommend a note taking wiki-like "super" application

I need a note taking wiki-like "super" application. I'll start with a rundown of applications that I've already evaluated and/or used:

Wikidpad

• Pros:
  • fast switching between the edit and view modes;
  • nice syntax (especially for pasting code snippets or just raw ASCII text, nice indenting visual clues);
  • it is standalone application that don't require server;
  • the wiki pages can be kept in flat text database;
  • easy drag-and-drop of file attachments (especially for image files).
• Cons:
  • doesn't have history/version control of the pages and the state of the wiki database as a whole;
  • doesn't have the concept of namespaces for the wiki pages;

MoinMoin wiki

• Pros:
  • nice syntax;
  • have standalone server (Python based) which makes it truly portable and standalone;
  • keeps the pages in flat files;
  • have a lots of nice plugins;
• Cons:
  • its a wiki == slow iterations of editing/taking notes, viewing, rince-repeat...
  • doesn't have version control integration

Trac

• Pros:
  • All of the features of the MoinMoin wiki, except the flat file database;
  • Version control integration: I can use the wiki changeset feature and the wiki pages as metadata of my personal codebase;
• Cons:
  • All of the general drawbacks of the wikis;
  • Not truly portable;

todolist2 (by AbstractSpoon)

• Pros:
  • fast, standalone todolist manager;
  • the tasks have this really nice and important for me feature of having an rich edit box for taking notes associated with the task with flipping between the task and the notes with a single key;
  • time tracking for the tasks;
• Cons:
  • doesn't have version control built-in (it has "simple" version control by just making an automatic backup copies of the project/data file with time stamp embedded in its name).
  • it's hard to filter the tasks by urgency (in the GTD terms, it doesn't have the concept of the containers of tasks: Inbox, Maybe, Next action for each project, etc).
  • it doesn't have cross-referencing/linking between the tasks in wiki-like fashion.

Thinking Rock

• Pros:
  • implements GTD almost perfectly;
  • it has notes for every action;
  • portable;
• Cons:
  • (Maybe because of the Java GUI) doesn't have simple Undo when editing text notes;
  • it's clunky when switching between the projects/actions tree and the editable notes editbox;
  • doesn't have version control;

MonkeyGTD/TiddlyWiki

• Pros:
  • truly standalone
  • almost 100% wiki
  • nice GTD implementation
• Cons:
  • it's little confusing when there is no easy or user-friendly way to see an overview of the current structure of the wiki pages
  • I'm not sure if it scales well when there is a lots of pages/data/text/attachments.
  • doesn't have source control integration;
  • I'm not sure about version control/pages history...

I want an application that has the following:

• the speed and the ease of edit/preview iteration cycle of wikidpad.
• the wiki pages and the associated attachments as they are (like wikidpad and MoinMoin).
• version control for the wiki pages (like MoinMoin or Trac).
• source control integration (like Trac).
• time tracking like todolist2 and the task/project nesting like todolist2 and ThinkingRock.
• the almost perfect GTD implementation of ThinkingRock or MonkeyGTD.

It's obvious that I haven't decided which one to use because for some reason my requirements are somehow orthogonal in the terms of the features that the aforementioned applications provide... not that the features are orthogonal or it is impossible or impractical... actually, I think that maybe wikidpad is the closest to my ideal, which means that I could:

• implement the features that I need (to add version control, GTD-life features/properties for the wiki pages themselves, source control integration), or
• continue to search and evaluate, or
• get some interesting and valuable opinions here.

ConnectedText has all the pros of Wikidpad and none of the cons. ConnectedText has a much superior query engine and contains semantic extensions not available in Wikidpad, and is much more stable.