In general, I haven't had any problem with program updates from the major software firms, other than a McAfee update deleting Spotify from my computer.
The updates are made primarily for security purposes, to protect your computer from flaws that may may your computer vulnerable to viruses and worms and such. Every once in a while, an update will have a functional improvement to your program - but most of the time, they're just security updates.
I'd advise accepting most updates, and setting Windows to automatically update. For other programs (like Adobe Reader), occasionally go to "Help" and select "check for updates" (or the like), and see if you're up-to-date. I know conspiracy theorists say otherwise, but most software manufacturers provide updates for your benefit, because they want you to be happy with their products so you'll buy from them again.

-Joe-