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..
Nice! You can find a lot of these by reading the Emacs info pages closely...never noticed that one.
My favorite "wish I had known about that sooner" part is iswitchb-mode -- it tremendously improves buffer switching, IMHO. (I usually filter the buffer list with iswitchb and then hold C-k to close buffers.) It makes the buffer switch prompt in the minibuffer behave like dmenu (http://www.suckless.org/programs/dmenu.html), for people who are already big fans of one or the other.
Also variously cool/vital: flyspell, keyboard macros, the mark and kill rings, abbrev, set-goal-column, C-x zzzzzz.
If you like abbrev, try out pabbrev, its even more awesome. (Theres also another predictive abbrevation mode that seems to have better UI, but I had difficulty getting it working in my "I will spend 30 minutes mucking with my .emacs" moment)