An artificial environment for the manufacture of chips in which the air has been scrubbed to remove almost all the matter normally floating around in air -- microorganisms, dust, hair, and the like.

Clean rooms are used with airlocks and bunny suits because even the slightest speck of dust can ruin a silicon wafer.

(idea)
When speaking of code, a clean room implementation of a piece of software is one created without using other code as an immediate reference guide. To create an alternate implementation of a protocol without getting sued, for example, one either avoids reading the code for a non-free version or waits a certain amount of time after reading it. This helps to keep a programmer from inadvertently using proprietary code.