I apologize in advance for a very long winded answer to what you thought would be a very simple question. Unfortunately, piecing together an entire operating system from many different bits in a coherent and unified manner is not exactly a trivial task. I'm currently working on my own Xen based distribution, I'll share my experience thus far (beyond Linux From Scratch):

1 - Decide on a scope and stick to it

If you have any hope of actually completing this project, you need write an explanation of what your new OS will be and do once its completed in a single paragraph. Print that out and tape it to your wall, directly in front of you. Read it, chant it, practice saying it backwards and whatever else may help you to keep it directly in front of any urge to succumb to feature creep.

2 - Decide on a package manager

This may be the single most important decision that you will make. You need to decide how you will maintain your operating system in regards to updates and new releases, even if you are the only subscriber. Anyone, including you who uses the new OS will surely find a need to install something that was not included in the base distribution. Even if you are pushing out an OS to power a kiosk, its critical for all deployments to keep themselves up to date in a sane and consistent manner.

I ended up going with apt-rpm because it offered the flexibility of the popular .rpm package format while leveraging apt's known sanity when it comes to dependencies. You may prefer using yum, apt with .deb packages, slackware style .tgz packages or your own format.

Decide on this quickly, because its going to dictate how you structure your build. Keep track of dependencies in each component so that its easy to roll packages later.

3 - Re-read your scope then configure your kernel

Avoid the kitchen sink syndrome when making a kernel. Look at what you want to accomplish and then decide what the kernel has to support. You will probably want full gadget support, compatibility with file systems from other popular operating systems, security hooks appropriate for people who do a lot of browsing, etc. You don't need to support crazy RAID configurations, advanced netfilter targets and minixfs, but wifi better work. You don't need 10GBE or infiniband support. Go through the kernel configuration carefully. If you can't justify including a module by its potential use, don't check it.

Avoid pulling in out of tree patches unless you absolutely need them. From time to time, people come up with new scheduling algorithms, experimental file systems, etc. It is very, very difficult to maintain a kernel that consumes from anything else but mainline.

There are exceptions, of course. If going out of tree is the only way to meet one of your goals stated in your scope. Just remain conscious of how much additional work you'll be making for yourself in the future.

4 - Re-read your scope then select your base userland

At the very minimum, you'll need a shell, the core utilities and an editor that works without an window manager. Paying attention to dependencies will tell you that you also need a C library and whatever else is needed to make the base commands work. As Eli answered, Linux From Scratch is a good resource to check. I also strongly suggest looking at the LSB (Linux standard base), this is a specification that lists common packages and components that are 'expected' to be included with any distribution. Don't follow the LSB as a standard, compare its suggestions against your scope. If the purpose of your OS does not necessitate inclusion of something and nothing you install will depend on it, don't include it.

5 - Re-read your scope and decide on a window system

Again, referring to the everything including the kitchen sink syndrome, try and resist the urge to just slap a stock install of KDE or GNOME on top of your base OS and call it done. Another common pitfall is to install a full blown version of either and work backwards by removing things that aren't needed. For the sake of sane dependencies, its really better to work on this from bottom up rather than top down.

Decide quickly on the UI toolkit that your distribution is going to favor and get it (with supporting libraries) in place. Define consistency in UIs quickly and stick to it. Nothing is more annoying than having 10 windows open that behave completely differently as far as controls go. When I see this, I diagnose the OS with multiple personality disorder and want to medicate its developer. There was just an uproar regarding Ubuntu moving window controls around, and they were doing it consistently .. the inconsistency was the behavior changing between versions. People get very upset if they can't immediately find a button or have to increase their mouse mileage.

6 - Re-read your scope and pick your applications

Avoid kitchen sink syndrome here as well. Choose your applications not only based on your scope and their popularity, but how easy they will be for you to maintain. Its very likely that you will be applying your own patches to them (even simple ones like messengers updating a blinking light on the toolbar).

Its important to keep every architecture that you want to support in mind as you select what you want to include. For instance, if Valgrind is your best friend, be aware that you won't be able to use it to debug issues on certain ARM platforms.

Pretend you are a company and will be an employee there. Does your company pass the Joel test? Consider a continuous integration system like Hudson, as well. It will save you lots of hair pulling as you progress.

As you begin unifying all of these components, you'll naturally be establishing your own SDK. Document it as you go, avoid breaking it on a whim (refer to your scope, always). Its perfectly acceptable to just let linux be linux , which turns your SDK more into formal guidelines than anything else.

In my case, I'm rather fortunate to be working on something that is designed strictly as a server OS. I don't have to deal with desktop caveats and I don't envy anyone who does.

7 - Additional suggestions

These are in random order, but noting them might save you some time:

Maintain patch sets to every line of upstream code that you modify, in numbered sequence. An example might be 00-make-bash-clairvoyant.patch , this allows you to maintain patches instead of entire forked repositories of upstream code. You'll thank yourself for this later.

, this allows you to maintain patches instead of entire forked repositories of upstream code. You'll thank yourself for this later. If a component has a testing suite, make sure you add tests for anything that you introduce. Its easy to just say "great, it works!" and leave it at that, keep in mind that you'll likely be adding even more later, which may break what you added previously.

Use whatever version control system is in use by the authors when pulling in upstream code. This makes merging of new code much, much simpler and shaves hours off of re-basing your patches.

Even if you think upstream authors won't be interested in your changes, at least alert them to the fact that they exist. Coordination is essential, even if you simply learn that a feature you just put in is already in planning and will be implemented differently in the future.

You may be convinced that you will be the only person to ever use your OS. Design it as though millions will use it, you never know. This kind of thinking helps avoid kludges.

Don't pull upstream alpha code, no matter what the temptation may be. Red Hat tried that, it did not work out well. Stick to stable releases unless you are pulling in bug fixes. Major bug fixes usually result in upstream releases, so make sure you watch and coordinate.

Remember that it's supposed to be fun.

Finally, realize that rolling an entire from-scratch distribution is exponentially more complex than forking an existing distribution and simply adding whatever you feel that it lacks. You need to reward yourself often by booting your OS and actually using it productively. If you get too frustrated, consistently confused or find yourself putting off work on it, consider making a lightweight fork of Debian or Ubuntu. You can then go back and duplicate it entirely from scratch. Its no different than prototyping an application in a simpler / rapid language first before writing it for real in something more difficult. If you want to go this route (first), gNewSense offers utilities to fork your own OS directly from Ubuntu. Note, by default, their utilities will strip any non free bits (including binary kernel blobs) from the resulting distro.

I strongly suggest going the completely from scratch route (first) because the experience that you will gain is far greater than making yet another fork. However, its also important that you actually complete your project. Best is subjective, do what works for you.

Good luck on your project, see you on distrowatch.