I though of this early on, but what I've been looking for is something with a mylar connection cable. For those not familiar, mylar is the flexible plastic circuitry used in places where flexabilty is key. For example, the N900 has flex connectors internally linking the LCD display and the main board. It's also used heavily in keyboards, including the N900 keyboard.

With the proper short micro USB mylar adapter, the "edge" coming out of the connector would be under 1mm. Throw a case on over it, and it wouldn't provide much leverage at all.

The issue then becomes making an output port available. You'd need enough space to handle the depth of a female micro USB port somewhere inside the case to pull that off, or a larger "shell" with space to do this. (Like a Mugen battery pack shell?) The N900 as it stands is so densely packed however, that I don't see any place with enough space to house such a connector without making the device physically larger.

If you're ok with losing the port all together (eg you just want to use it to charge) the mylar solution may be a good way to go. You could probably even create a mylar sheet with a loop large enough to do inductive charging. Most of my data transfer is via wifi or bluetooth, so for me this would be an acceptable solution.