It's also pretty annoying to try to reinstall them if you ever do need them. Most aren't available on Apple's website or any (public) torrent trackers. You have to do something like use Pacifist to dig around .pkgs on the installation disk / image.
I've split my Applications folder into subdirectories, using a ridiculous Windows drive name-like naming scheme. The unused or rarely used bundled apps in "/Applications/B". (A = main, S = secondary, U = utilities, D = developer, N = new, O = old, T = tested, L = library.)
Solve your neat issues by making an /Apps or ~/Applications or something else, and but Aliases or links from there to the few you do use. Then just ignore /Applications.
Some dialogs for choosing applications only include things in /Applications and ~/Applications. (+ some in CoreServices.) Many apps will also nag that they can move themselves to the Applications folder on the first launch. Installers will still put things to /Applications. And aliases aren't that neat anyway...