Settings Manager
I believe it's important that we don't let this become like other open-source operating systems - cluttered with various setting files. We need to create one settings manager that all programs will store their settings in. With Ubuntu, if you want to change the font everywhere you have to change it in appearance preferences, gnome-terminal, ~/.profile, and others. We need to avoid madness like this.
Another problem with common setting managers is that they don't integrate very well with the OS - there's no way to make a shortcut to the current desktop background for example. We should store our settings in files, one setting per file, that way it would be possible to take advantage of links and any other future filesystem features.

Comments
Re: Settings Manager
With fonts, this is pretty much the case as far as I know. Third-party toolkits like Qt might use their own settings though. Is there any particular issue in Haiku you have in mind? I noticed web browsers tend to go their own path with rendering of text in web pages, this could get annoying perhaps.
Re: Settings Manager
It's not an issue in Haiku. All personal settings are stored in ~/config/settings/ (a few system wide settings are in /boot/common/settings/). If some app doesn't comply to this or doesn't respect system settings (mostly badly done ports) it should be shunned until it does.
Regards,
Humdinger
Re: Settings Manager
No I didn't have any particular issue in mind, it's just that other open source operating systems started out using just /etc/default, but then things like gconf came along and ruined everything. We need to strongly enforce that settings should all be stored in one place to make it easy to backup, restore, copy and administrate them.
I made a post on Ubuntu forums a while ago, but the truth is, something that big is never going to happen once an OS is up and running, which is why I'm posting it here.