The Customizable Sidebar plugin does allow you to change order of custom commands. I’ve implemented the feature myself.
Please read my original comment again - you first need to hide all auto-added commands and then add your own commands that can be reordered with arrow buttons. You also need to have up-to-date version of the plugin.
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Thanks for adding that detail. As far as I’m aware, most people in this thread are looking to customize the order of anything in the sidebar, not just custom commands added by the Customizable Sidebar plugin. For that, Obsidian Bartender is still the recommendation.
I think you misunderstood. You can customize order of any commands. You just need to add them to the sidebar myself and hide original commands, but in the end they look and are practically the same.
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For my use-case, I use both plugins together to achieve different but harmonious things.
I use Customizable-Sidebar to hide things that I do not want & to add custom commands.
I use Obsidian-Bartender to rearrange icons in the sidebar with quick and simple drag-and-drop functionality, without the need to open the plugin settings to rearrange (as is the case with Customizable-Sidebar), or, as you recommended, having to remove all sidebar icons first and readding them afterwards so that they can be rearranged. Perhaps that makes sense for someone who wants to start fresh and re-add only what they want, one by one, whereas for me, I wanted most of what I had in the sidebar, I just needed easy functionaility to rearrange them.
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Bartender is a good idea, but it is pretty buggy. It does not like to move files around. Folders fare better, but I named one folder Index and tried to move it up. It leaves a pixel remnant but goes back where it came from. Definitely beta.
Normally when you drag it only wants you to drop one item inside another folder. This is the behavior I am getting but only for some folders. For example I have a folder named Indexes and as I move it, it only shows "move into folder xyz’. If I move it to the top it will ‘land’ but then it leaves a pixel remnant and goes back where it came from.
sure, I think I also need it.
Dear Obsidian core-team, Obsidian is ultra-powerful but to my opinion the UI is becoming really clumsy. So many features and so many features and no easy way to configure the icon-bar simply and reliably. I am not an expert programmer but I have the impression that adding a core option panel simply to pick the order of any icons would not take long and would make the UI so easier to use for those power user with many plugins and an overcrowded Obsidian left-icon bar.
Please please please 
Surfacing this post again as well, having options to order and hide/show these icons seems pretty critical for users to scale/customize the UI
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Actually, bartender isn’t meant to move files or folders. It only moves items in the sidebar (toolbar icons) and status bar (at the bottom of the window, like word counts, etc.). It’s the core Obsidian plugin File Explorer that is used to move files and folders around a vault. There are also community plugins to do this (i.e., alternate file explorers). 
for the Customizable-Sidebar plugin suggestion. Exactly what I was looking for until ordering items is built-in to Obsidian.
Works for me on MacOS and iOS. Finally my iOS sidebar doesn’t re-order on its own every few days.
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I can’t find either plugin by those names in the community plug-ins section in settings. I searched for Sidebar and for Customizable respectively and nothing came up that matches those names.
Have they been discontinued or are they now called something else?
The Commander plugin is awesome, but it’s a bit cumbersome to use. You first need to deactivate all existing icons and then add them all back manually and find fitting icons for them. Also, you can only use the standard icons, not the custom icons that come with some of the plugins. I’d really prefer to be able to just rearrange the icons in my bars manually. Similar to how you can now rearrange the tab headers in the sidebars which was also not possible in earlier versions.
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I just came up with this workaround. Open obsidian and go to settings/appearance/CSS snipets and add the code below to the .css file. It will higlight the daily note icon. Feel free to customise to your needs
div[aria-label = "Open today's daily note"]{
color: yellow;
}
Final result:
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Obsidian Bartender is still in beta or otherwise not approved as a community plugin yet. Here’s the repo, unfortunately, dragging to rearrange hasn’t worked for me on 1.0+ yet.
Customizable Sidebar has been archived and replaced by Commander. It’s what I’m using now but it does have the drawbacks mentioned two posts up.
The Commander plugin is fantastic. Many thanks as it resolves the issue of overpopulating the sidebar with too many icons.
FYI, v1.1.0 now has it built in, works well
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Yay! 
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