Choice is often made largely on perception and culture, rather than concrete data. And, making a choice based on concrete data is difficult when you consider the complexity of a modern OS, all the issues associated with porting it to custom hardware, and unknown future requirements. Even from an application perspective, things change over the life of a project. Requirements come and go. You find yourself doing things you never thought you would, especially if they are possible. The ubiquitous USB and network ports open a lot of possibilities -- for example adding Cell modem support or printer support. Flash based storage makes in-field software updates the standard mode of operation. And in the end, each solution has its strengths and weaknesses -- there is no magic bullet that is the best in all cases.
When considering Embedded Linux development, I often use the iceberg analogy; what you see going into a project is the part above the water. These are the pieces your application interacts with, drivers you need to customize, the part you understand. The other 90% is under water, and herein lies a great deal of variability. Quality issues with drivers or not being able to find a driver for something you may want to support in the future can easily swamp known parts of the project. There are very few people who have a lot of experience with both WinCE and Linux solutions, hence the tendency to go with what is comfortable (or what managers are comfortable with), or what we have experience with. Below are thoughts on a number of aspects to consider:
SYSTEM SOFTWARE DEVELOPMENT
Questions in this realm include CPU support, driver quality, in field software updates, filesystem support, driver availability, etc. One of the changes that has happened in the past two years, is CPU vendors are now porting Linux to their new chips as the first OS. Before, the OS porting was typically done by Linux software companies such as MontaVista, or community efforts. As a result, the Linux kernel now supports most mainstream embedded cpus with few additional patches. This is radically different than the situation 5 years ago. Because many people are using the same source code, issues get fixed, and often are contributed back to the mainstream source. With WinCE, the BSP/driver support tends to be more of a reference implementation, and then OEM/users take it, fix any issues, and that is where the fixes tend to stay.
From a system perspective, it is very important to consider flexibility for future needs. Just because it is not a requirement now does not mean it will not be a requirement in the future. Obtaining driver support for a peripheral may be nearly impossible, or be too large an effort to make it practical.
Most people give very little thought to the build system, or never look much beyond the thought that "if there is a nice gui wrapped around the tool, it must be easy". OpenEmbedded is very popular way to build embedded Linux products, and has recently been endorsed as the technology base of MontaVista's Linux 6 product, and is generally considered "hard to use" by new users. While WinCE build tools look simpler on the surface (the 10% above water), you still have the problem of what happens when I need to customize something, implement complex features such as software updates, etc. To build a production system with production grade features, you still need someone on your team who understands the OS and can work at the detail level of both the operating system, and the build system. With either WinCE or Embedded Linux, this generally means companies either need to have experienced developers in house, or hire experts to do portions of the system software development. System software development is not the same as application development, and is generally not something you want to take on with no experience unless you have a lot of time. It is quite common for companies to hire expert help for the first couple projects, and then do follow-on projects in-house. Another feature to consider is parallel build support. With quad core workstations becoming the standard, is it a big deal that a full build can be done in 1.2 hours versus 8? How flexible is the build system at pulling and building source code from various sources such as diverse revision control systems, etc.
Embedded processors are becoming increasingly complex. It is no longer good enough to just have the cpu running. If you consider the OMAP3 cpu family from TI, then you have to ask the following questions: are there libraries available for the 3D acceleration engine, and can I even get them without being committing to millions of units per year? Is there support for the DSP bridge? What is the cost of all this? On a recent project I was involved in, a basic WinCE BSP for the Atmel AT91SAM9260 cost $7000. In terms of developer time, this is not much, but you have to also consider the on-going costs of maintenance, upgrading to new versions of the operating system, etc.
APPLICATION DEVELOPMENT
Both Embedded Linux and WinCE support a range of application libraries and programming languages. C and C++ are well supported. Most business type applications are moving to C# in the WinCE world. Linux has Mono, which provides extensive support for .NET technologies and runs very well in embedded Linux systems. There are numerous Java development environments available for Embedded Linux. One area where you do run into differences is graphics libraries. Generally the Microsoft graphical APIs are not well supported on Linux, so if you have a large application team that are die-hard windows GUI programmers, then perhaps WinCE makes sense. However, there are many options for GUI toolkits that run on both Windows PCs and Embedded Linux devices. Some examples include GTK+, Qt, wxWidgets, etc. The Gimp is an example of a GTK+ application that runs on windows, plus there are many others. The are C# bindings to GTK+ and Qt. Another feature that seems to be coming on strong in the WinCE space is the Windows Communication Foundation (WCF). But again, there are projects to bring WCF to Mono, depending what portions you need. Embedded Linux support for scripting languages like Python is very good, and Python runs very well on 200MHz ARM processors.
There is often the perception that WinCE is realtime, and Linux is not. Linux realtime support is decent in the stock kernels with the PREEMPT option, and real-time support is excellent with the addition of a relatively small real-time patch. You can easily attain sub millisecond timing with Linux. This is something that has changed in the past couple years with the merging of real-time functionality into the stock kernel.
DEVELOPMENT FLOW
In a productive environment, most advanced embedded applications are developed and debugged on a PC, not the target hardware. Even in setups where remote debugging on a target system works well, debugging an application on workstation works better. So the fact that one solution has nice on-target debugging, where the other does not is not really relevant. For data centric systems, it is common to have simulation modes where the application can be tested without connection to real I/O. With both Linux and WinCE applications, application programing for an embedded device is similar to programming for a PC. Embedded Linux takes this a step further. Because embedded Linux technology is the same as desktop, and server Linux technology, almost everything developed for desktop/server (including system software) is available for embedded for free. This means very complete driver support (see USB cell modem and printer examples above), robust file system support, memory management, etc. The breadth of options for Linux is astounding, but some may consider this a negative point, and would prefer a more integrated solution like Windows CE where everything comes from one place. There is a loss of flexibility, but in some cases, the tradeoff might be worth it. For an example of the number of packages that can be build for Embedded Linux systems using Openembedded, see.
GUI TRENDS
It is important to consider trends for embedded devices with small displays being driven by Cell Phones (iPhone, Palm Pre, etc). Standard GUI widgets that are common in desktop systems (dialog boxes, check boxes, pull down lists, etc) do not cut it for modern embedded systems. So, it will be important to consider support for 3D effects, and widget libraries designed to be used by touch screen devices. The Clutter library is an example of this type of support.
REMOTE SUPPORT
Going back to the issue of debugging tools, most people stop at the scenario where the device is setting next to a workstation in the lab. But what about when you need to troubleshoot a device that is being beta-tested half-way around the world? That is where a command-line debugger like Gdb is an advantage, and not a disadvantage. And how do you connect to the device if you don't have support for cell modems in New Zealand, or an efficient connection mechanism like ssh for shell access and transferring files?
SUMMARY
Selecting any advanced technology is not a simple task, and is fairly difficult to do even with experience. So it is important to be asking the right questions, and looking at the decision from many angles. Hopefully this article can help in that.