I also hated to have all my windows flying around when I would (un)plug my MacBook Pro from external devices... Some time ago I discovered Stay (http://cordlessdog.com/stay/) and now I have no more problems with that. It is great, you can define position of windows for all your different setups (profiles). In my case I mostly have two setups, at office (where I work most of my time) I plug my MacBook Pro to an external display and when I am at home I work directly on the MacBook and sometimes I connect it to another external display.

I am a big fan of being able to just work whenever I want on my computer... but I also am extremely big fan of plugging it to external displays and use ergonomic devices, and I try to use them as much as I can. At my office I use a Kinesis Freestyle and a trackball, and am very happy since I started using it. We spend so much time in these "positions" that we should minimize possibilities of having problems and be confortable... at the end we want to keep doing this for long time ;)