The desktop client just integrates really well with my workflow. When I have to move from one app to the browser and open up a new tab it takes me out of my current mode of operation. It's a subtle nuance in liking the desktop client better than the browser but I think it's important. You also contend with other distractions in the browser. All hell breaks loose when I see my bookmarks to HN, Reddit, Facebook, etc. and there goes my productivity...
For our company, with just a couple of founders, chat rooms wouldn't make sense because we want everyone to know everything. We'd just have one master chat room. In Yammer, hashtags provide a similar feature to chat rooms, although all conversations are aggregated into one stream. I guess we could have separate chat rooms for checkins, bugs, etc. but now I'm flipping between tabs when I could have just tagged by comment with the right hashtag.