That's a pretty lame way to do it... renaming anything you want to run from the Finder as ".command"? That's really a kludge. I can't believe you'd consider this a good solution. What if you want to call a system binary? You could probably make a symbolic link or a short script wrapper, but that's still way kludgy.
The Finder has the 'file' utility available from Unix. It should just call that utility or integrate the code... if it realizes that this is an executable file, it should open it automatically, possibly firing up Terminal to do so. Obviously I don't have access to the Finder code, but I just can't imagine that this would be difficult to do.
The 'open' command, on the other hand, is pretty slick, I appreciate the other poster mentioning it. It seems like an 'open .' alias will be really useful; cd into an app directory, poke around, and then maybe 'run' to launch it.
I stand behind my premise that Aqua and the Finder are not well-integrated with Unix. I have heard nothing but praise for NeXTStep, so I'm assuming the reason the marriage here is so bad is because of legacy Mac compatibility issues.
I think OSX would be a BIG deal for a Mac user who wants to run existing apps on a real OS, but for a Unix geek... it's just not that hot. Yet.