I like to play with the y axis inverted. Unfortunately, the only thing you can do in the game is to invert the y and the x axis both. Are there any known workarounds? Any help would be great - not to mention it would save my keyboard, whose keys I have been smashing in frustration.

You can try the following:

1. Xpadder

WARNING: You Must Pay For This Program.

You may purchase / acquire a copy of Xpadder, and remap the keyboard controls to a gamepad. During this process, when mapping the mouse to the right analog stick, you have the following options: Regular mouse, Inverted X, Inverted Y, and Inverted X+Y.

The gamepad I use for my PC is an old 'Madkatz' Xbox 360 wired controller, which has a Right Analog Y-axis inversion switch on the back that I use all the time. Having the hardware do the inversion for you is always the best solution, I've found.

That being said I tested the Xpadder method using the X axis inversion, and it does seem to work.
Do note, however: I have noticed other message boards / threads stating they installed an x inverter program, only to have it stop working randomly.

2. Joy 2 Key

Same basic function as Xpadder - this program maps keyboard and mouse input to a game pad. The Gui is extremely basic, and is much more difficult / annoying to set up. But it's free.

I did not bother to test this program after seeing the GUI.

3. Polynomial's Mouse Inverter - v1.0

File Location: sendspace.com/file/zjuwfv

I found this after a quick Google search. It was posted on a forum in which the original poster was looking for a way to completely flip a Mouse's X & Y axis' in windows for a client with severe dyslexia.

Requires Microsoft .NET framework 4.0 to run.
WARNING: This program will effect all mouse movement on the system after being enabled.
This program does allow you to chose which axis to invert upon start up.

However, it has been mentioned on the forums here on GoG, the Steam Forums, and elsewhere that Beyond Good and Evil will actively ignore this program's mouse inversion. I myself have had the program work properly once, subsequent uses of the program have caused windows file explorer to hang after running (Win7 x64).
Use at own risk.

4. Axis inverting or rotating mouse filter driver by MAF-Soft

Website: maf-soft.de/mafmouse/
WARNING: You Must Pay For This Program.

The website lists Beyond Good and Evil as #1 on it's "Hall of Shame". I assume this means it has been tested by the author to guarantee functionality. Since one would need to contact the software author for the price of the software, this question would best be asked during first contact.

I have not tried this software, and have no desire to do so.

5. AutoHotKey (AHK)

Website: autohotkey.com/board/topic/17828-invert-mouse-axis/
Of Note: autohotkey.com/board/topic/17828-invert-mouse-axis/page-2 - First entry

I found this entry in the Autohotkey community support forum. Opening post was asking how to invert the mouse axis of a 'mouse like device' the person fabricated themselves. However, the first entry of the second page has a script with 3 global Boolean variables to alter the mouse cursor's behavior: Swap_xy, Invert_x, and Invert_y.

Further entries on page 2 refine the script in various ways.
I have not tested this method in the slightest.

6. SakasaMouse

File Location: Download via CNet.com

This program is described as a 'joke program', and states it's purpose as mouse inversion. It is mentioned both on the Autohotkey site, and on the Steam Forums for Beyond Good and Evil. However, according to the Steam Forum thread, it is neither a global, nor reliable solution. Some reported it worked, only to come back saying it no longer worked. Some stated it did not work at all. One Steam Forum user went so far as to say the reason the program did not work is due to Beyond Good and Evil ignoring the system registry values for inverted x / y input.

Use at own risk.
I have not tested this program.

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Frankly, the options seem to be thus:
A) Get used to standard mouse input
B) Use a gamepad with either Xpadder or Joy2key.
C) Muck about with various software which may work, may randomly cease working at any time, or may incite changes that are ignored by the game upon launch.

Hope this helps.
-JJ

For those of you having this problem, and own an Xbox 360 Joypad there is an easy fix (well, relatively easy) using joy2key (mentioned in the list by the poster above, but not tested by him/her)

joytokey dot-net-slash-en (gog wont let me post a link)

Extract the program to wherever (I put it in a subfolder in the game folder), and run it before starting the game (after setting your bindings of course). I created a shortcut in the same location as the game shortcut, or you can just leave it running in the background.

Whats nice about this little program is you can associate a binding profile per game. Be sure to point the profile and game shortcut to BGE.exe and not the default launcher, otherwise it wont work.
As a heads up, the binding for the camera is done through stick 2, 'Edit button assignment' for each direction, and use the 'Cursor Movement' sliders to define the camera axis and direction. For example, -100 would be x-axis Left.

Gui is not so bad, took me about 5 minutes to figure it all out and get it working.
Camera/stick sensitivity can be adjusted in game via mouse sensitivity.

Works 100%
If your camera sees a bit of stuttering, change the internal processing speed higher under settings.
Please note I take no responsibility for any consequences of using this method, just trying to help.

Good luck and enjoy the game!

I have to add that it is shameful Ubisoft/Developer have not fixed this to this day :-(
NOTE - Gog would not let me upload my .cfg file, if I get any interest I can put it up on a file hosting service.

I just couldn't deal with the controls in this when I bought it years ago and I purchased MAF Mouse. It did the job perfectly. Not sure how well it would go if you have brand specific mouse drivers installed though instead of the generic windows driver I was using back then.