Holding my breath for a server-side CSS fix has only produced dizziness with visual aura, so instead I made a bookmarklet which applies a crude CSS fix when clicked:
Bookmarklet: fixYCpre
Drag this to your bookmark bar, then click when encountering a PRE-overwide News.YC page. PRE elements will be restyled to a fixed width, and a hover-activated horizontal scrollbar will offer access to any overflow.
(The most important part is the applied 'max-width'. The 'padding' helps ensure the scrollbar appears even for 1-line PREs. The white 'background-color' is just a visual flourish I like.)
Confirmed working in FF3, Safari3, Chrome. Doesn't work in IE7 and life is too short to waste wrestling with IE eccentricities.