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I just uploaded version 0.5.1 to extras-devel which should improve the sizing and spacing issue.
Could you please try if this version fixes your issue?

Still, I am not 100% satisfied with the placement of the clock inside the rounded rectangle.
Though, this version should avoid the "cut-off" problems you are experiencing.

It's fixed in the new version.

I can't attach the old look because I can't post the ss, it contains private info. But if you are interested, I can edit the image and post when at home tonight.

Good to hear.
Well, as long as it's fixed it's fine for me.
So, there is no need to send a screenshot.

Just uploaded version 0.6.0 which adds an option to display values as gray code.
Though, be aware that this looks best for displays which do the "complete cycle" from 0 to (2 to the power of n) - 1 (n being the number of digits).
Hence, this looks best for the two Unix Time displays.

For the other displays which display the local time there are "jumps" visible in which more than one LED changes.
E.g.: the seconds and minute displays perform such a "jump" when changing from 59 to 0.

xD i broke a virtual clock...
i was expiremnting with the size and spacing and it became too big, and the settings icon is now out of reach... Is there a way to fix that?
thank you!

Try to execute the following as user in an xterm:
This should reset Binary Clock to its defaults.

Thank you that fixed it

Alright,
this is for the adventurous:
I made a status area plugin which replaces the standard clock in the status area with a binary version.
Please be aware that this package is still a work in progress and hence may feature a number of pitfalls.

If you want to try it you can find the latest version in extras-devel.
The package is called "binaryclock-plugin".
Installing this will replace the standard clock with a binary version.
To get the standard clock back just uninstall binaryclock-plugin as usual via the application manager.

I'll open a dedicated "announce-thread" once I think this is mature enough to be released into the wild.
So long, your comments are highly appreciated.
Note: a settings dialog is available via the status area menu.
Though, the settings are not stored yet.
Consequently, the changes are lost after, e.g., a reboot.

P.S.: Currently, somehow the uploaded package description and hence the package website is way messed up.
The application manager displays the description correctly, though.
I am working on getting this fixed.

Question: Is the normal clock applet in the status bar open source? If not, I would use this as further benefit to my following feature request for the status bar version, though I think it's meritable enough in itself:

Also add normal 12 and 24 hour time displays. This would allow us users to switch casually to 12/24 hour and binary displays when desired without either A, editing the /etc/hildon-desktop/status-menu.plugins file, or B uninstalling and reinstalling the applet.

It also allows for the adding of the seconds on/off to the normal-numbers display. You could probably release the thing as "Advanced Clock Applet" or something (in the pattern of Advanced Power and Advanced Interface Switcher, but your app, your name, obviously). Possibly release both the simple Binary Clock, and the more feature-ladden version, IF you like the aesthetic of keeping them separate, or want the name of the more feature-ladden version to be more representative of the applet, without sacrificing the Binary Clock name. *Shrug*

At any rate, I am not pushing for getting this done now, because it can obviously wait. But I do think that in the long term, it would be great to see this clock go that way, because it makes it versatile enough that it can serve as a clock replacement for everyone who's not completely happy with the normal display, rather than just those who like the binary clock. (Don't get me wrong, I like it too, or I wouldn't have installed it. But I also like the versatility of being able to switch with the press of a settings option, and being able to have people not versed in binary read the time if I happen to let them fiddle with my phone. :P )

Also, quick second request: Recently MohammadAG came out with a mod for Hildon-Home and Hildon-Desktop that allowed you to open the status bar's menu from any application in portrait mode (by default, pressing on the status bar icons area does nothing in portrait mode). This allows some much greater versatility in the form of, say, turning flashlight on/off and adjusting brightness from Simple Brightness Applet when in portrait mode. However, while the status menu works wonderfully in portrait mode, most (scratch that - all that I use) applets are not themselves coded to work in both portrait and landscape. So, while your Binary Clock settings button appears in the status menu when it's brought up in portrait mode, pressing on it forces the entire screen into landscape, because that's the only mode the pop-up menu itself has.

Now, I've looked at the code and I am not well-versed in python enough to fully get what's going on, or how to do this, or else I'd try myself and submit a patch to you myself, so: I'm requesting that you add portrait support (maybe with auto rotation... probably ideal if it can auto rotate, but I'm sure someone out there won't like it) to the pop-up settings menu that comes out when you press the status menu Binary Clock button, if it's possible and Hildon itself doesn't impose some restriction on that.

At the same time, if you pull off the aforementioned pop-up menu from-status-menu-applet auto-rotation/portrait-support, that same python code would be helpful for both the Advanced Power and Advanced Interface Switcher applets, and Live Focus (the actual package name is something odd, but I know it's written in Python too) could use it, and I'm sure there's a bunch of other python status applets that would benefit from this when combined with the newly-emerged portrait mode status-menu usability.