Someone should mention package manager performance. Searching for a package in an Arch system will take a long time (10s or more) except on relatively fresh installs. It may have been fixed by now, but it was a serious point of irritation.
Were you using XFS at the time? Search has never been a problem for me even on multi year old installs, but there was (is?) something about XFS that made pacman slow to a crawl.
Nope. The problem happened on multiple systems (i386, x64) regardless of filesystem (ext3, reiser), although problems only start after a few months. I found a bug in the bug tracker for it with multiple people confirming it and the "solution" was to wipe the package database manually every once in a while.