Whew, leaving emacs open for three months? That's intense. I've had uptimes of up to a year, but I knew I was totally wrong to do so and it wasn't in a corporate environment as this sounds to be ;-)
One of Steve Yegge's old rants includes the suggestion that some of his favourite systems are those that have both extensible-while-running and doesn't-crash - one being emacs.
Uptimes of up to a year aren't totally wrong - having to shut down and close everything to manually work around some memory leaks and gradual flakiness or to guard against crashes isn't a great or desirable feature, even if it is extremely common.
I was implicitly referring to routine kernel updates (desirable on most OS - though not all), or other key software updates (especially on OS X or Windows) - rather than forced restarts for stability reasons.
I guess it depends on your operating system, but there are few where it'd be good operational policy to not have key system updates at least a few times a year. They do exist, of course..