Adobe Reader -- Foxit Reader is faster, smaller, and does the same.
Apple -- I hate the Apple Updater for Windows. It keeps coming back and wants me to download QuickTime and iTunes.
Windows Update -- It's fine, besides the restart part. That can be disabled either through FARR, or one of the methods here
RealPlayer -- FAILS EPICALLY
Java -- Not that bad. You can uncheck the Yahoo! toolbar, and disable automatic updates if you want.
Yahoo! -- Their mail is great. For the messenger, I use Pidgin.
Norton AntiVirus -- I've heard a couple of good reviews, but it's SO MEMORY-HOGGING!
Preinstalled software bundles -- I uninstall everything I understand. The only good thing I ever got out of it was PowerDvd, which VLC is an alternative for.
Outlook -- Thunderbird.
Flash -- Flash games are cool, but I hate all-flash websites. They're so slow!