I went through the same issue, got tired of taking my gel case on & off because even with the spacer removed on the car dock, placing the phone in was a hassle. Inevitably, I dropped my phone (a couple of times) while getting out of the car, and of course it wasn't wearing a case. I have searched up/down/sideways for a case that will fit in the car dock and believe me, there is none.
I got the idea of dremmeling the dock from someone on the android forums, who took the approach of heating the dock with a torch and opening it up enough to fit a case. I took the dremmel approach which definitely left evidence of DIY'ing, but at least I have a working dock which will fit just about any case. I'm using it with VZW's leather case. Not to feather my own cap, but I don't think the damage is as evident as taking the torching approach.
I started by shaving off the 2 nubs on the bottom rear of the face, which did not allow the encased phone to go into the USB port. After that though, the front lip was still preventing proper seating, so I had to take the dremmel to the lip, using a gel case for the mockup. I took the dock apart to avoid any potential damage to the USB connector via a slip of the dremmel or from plastic shavings. It's pretty easy - undo the 4 screws in the back, and carefully pry the tabs on top. Be mindful that there is a 3rd tab on the inside, around the middle of the dock, but it did not prove to be a problem when pulling it apart.
After I put the leather case on, I had to finish shaving off the side lips in order to avoid the lips pinching and scratching the leather. However, for those of you who intend to use a thinner case, you may not have to go so extreme.
The only remaining issue is that the phone cannot sit flat against the dock because of the protruding corner of the top clamp's elbow (seen on the last pic). I haven't decided whether to shave it because that piece of the mechanism seems to be hollow plastic, and as it is, it holds the phone sufficiently well.
Here are the pics of the "final" work (although I may end up deciding to take a spray can to the face but IMHO, it's really not necessary. Hope this helps some of you in protecting your phone while being able to take advantage of the dock. As far as the home multimedia dock, I'm not going to bother with it. It's going up on craigslist as soon as my custom made Mikradle comes in...
