Objective-C Documentation Generators: HeaderDoc vs. Doxygen vs. AppleDoc
Xcode 5 will now parse your comments to search for documentation and display it:
You don't have to use appledoc or doxygen anymore (at least when you don't want to export your docs). More information can be found here
I'm the author of appledoc, so this answer may be biased :) I tried all mentioned generators though (and more) but got frustrated as none produced results I wanted to have (similar goals as you).
According your points (I only mention appledoc and doxygen, I don't recollect headerdoc that well):
Consistent look: appledoc out of the box, other need to tweak css, but probably doable.
Generation of documentation sets (for Xcode references): appledoc full support for searchable and option-clickable documentation out of the box, doxygen generates xml and makefile which you need to invoke yourself. Additionally appledoc supports published docsets out of the box.
Categories: appledoc allows you to merge categories to known classes or leave them separate, foundation & other apple class categories are listed separately in index file. doxygen: this wasn't working best when I tried it.
Custom reference pages: appledoc supports out of the box using either markdown or custom html, doxygen: you can include custom documentation to main page, don't know if you can include more pages.
Easy command line: depends how you look at it: appledoc can take all arguments through command line switches (but also supports optional global and project settings plist files) so it should be very easy to integrate with build scripts. doxygen requires usage of configuration file to setup all parameters.
Large codebases: all tools should support this, although didn't compare timewise. Also not sure if any tool supports cached values (running over previously collected data in order to save some time) - I am looking into adding this for next major release.
It's some time since I tried using other tools, so above mentioned issues with doxygen/headerdoc may have been addressed! appledoc itself also has disadvantages: like you mention there's no support for enums, structs, functions etc (there was some work done in this direction, check this fork), and it has it's own set of issues that may prevent you using it, depending your requirements.
I am currently working on major update that will cover most glaring issues, including support for enums, structs etc. I'm regularly pushing new stuff to experimental branch as soon as I finish larger chunks and make it stable enough, so you can follow the progress. But it's still very early and progress depends on my time so it may take quite a while until working solution.
As the creator and lead developer of doxygen, let me also provide my perspective
(obviously biased as well ;-)
If you are looking for a 100% faithful replica of Apple's own documentation style, then AppleDoc is a better choice in that respect. With doxygen you'll have a hard time to get that exact same look, so I would not recommend to try.
With respect to Xcode docsets; Apple provides instructions how to set that up with doxygen (written in the time Xcode 3 was released). For Xcode 4 there is also a nice guide how to integrate doxygen.
As of version 1.8.0, doxygen supports Markdown markup, as well a large number of additional markup commands.
With doxygen you can include documentation on the main page (@mainpage) as well as on subpages (using @subpage or @page). Inside a page you can create sections and subsections. In fact, doxygen's user manual was completely written using doxygen. Besides that, you can group classes or functions together (using @defgroup and @ingroup) and inside a class make custom sections (using @name).
Doxygen uses a configuration file as input. You can generate a template with default values using doxygen -g or use a graphical editor to create and edit one. You can also pipe options through doxygen via a script using doxygen - (see question 17 of the FAQ for an example)
Doxygen is not limited to Objective-C, it supports a large range of languages including C, C++, and Java. Doxygen is also not limited to the Mac platform, e.g. it runs on Windows and Linux too. Doxygen's output also supports more than just HTML; you can generate PDF output (via LaTeX) or RTF and man pages.
Doxygen also goes beyond pure documentation; doxygen can create various graphs and diagrams from the source code (see the dot related options). Doxygen can also create a browsable and syntax highlighted version of your code, and cross-reference that with the documentation (see the source browser related options).
Doxygen is very fast for small to medium sized projects (the diagram generation can be slow though, but nowadays runs on multiple CPU cores in parallel and graphs from one run are reused in the next run). For very large projects (e.g. millions of lines of code) doxygen allows the projects to be split into multiple parts and can then link the parts together as I explained here.
A nice real-life example of using doxygen for Objective-C can be found here.
The development of doxygen highly depends on user feedback. We have an active mailing list for questions and discussions and a bug tracker for both bugs and feature requests.
Most users of doxygen use it for C and C++ code, so naturally these languages have the most mature support and the output is more tuned towards the features and needs for these languages. That said, also wishes for and issues with other languages are taken seriously.
Note that I do nearly all doxygen development and most testing on a Mac myself.