We've all seen Google Gmail's "Set the time back", and YouTube's "Rick Roll Suggested" on the front page.
How about lesser known site pranks:
Check out these awesome and cheap biometric readers, or
A USB paternity test?
My favorite real-life April Fools was to convince someone they forgot to reset their clocks, and were an hour late to work. Ah, the early 90s when people would still fall for that.