We've been using a custom three column layout that Christopher developed way back when, but recently we've been tweaking it considerably, to include new features such as video support, stylesheet switching, custom search form and IE support. It's now similar to Zen in many ways and provides context/content specific classes and ids for ease of styling. We have plans for the future to create a more flexible theme based on CSS frameworks.
We have our own custom install profile that configures things like TinyMCE and CCK settings as well as setting up an admin user etc.
We are primarily a Mac/Adobe shop, so we have been using Dreamweaver up to now, however we sometimes use TextMate for new projects or projects that don't require a check-in/check-out capability. With the prospect of version control tools coming in the future we will be reviewing and reassessing. I know there are some hardcode VIM and Emacs users out there, we promise we'll consider both :)
Historically we have been a single developer shop with no need for a version control system as most sites were developed and then rolled out without need to many updates. However with the addition of more custom modules, working on much larger sites and the expansion of our team we now feel it necessary to implement some sort of version control system. Having seen some of these in action at DrupalCon, we will be working to have something running in a few months.
We use the standard modules such as CCK, Views etc. but also have the following custom modules:
Mobile Detection Module
I've recently finished a rough beta version of a mobile redirection module which uses this code to detect the user agent and then redirects to a specified URL. In most case we use a sub-domain folder like /sites/m.example.com and configure the settings.php to use a separate theme. We'll release this at some point also when it meets drupal's code and module development standards, not that it doesn't already but we need to make it less site specific.
Block Class extension
I wrote an extension to the block class module that allows the user to choose from a specified list of block class options, rather than typing one in.
Node title length
In some cases, to stop the design from breaking, we need to ensure that the node title lengths are restricted to a certain maximum. This module allows you to choose the content types to apply the restriction to and does the necessary validation.
CSS Image Replacement
Chris wrote a totally awesome tool that we then roughly ported to a module that uses CSS to do image replacement. For now that's all I can say, we'll be working on releasing it in the wild at some point but it rocks and relies on GD libraries and CSS definitions to create images to replace text.