An amalgam of "yak shaving" and "shaving yoctoseconds". This line is commonly mistranscribed as "shaving yoctoseconds".
"Yoctoseconds" - Second smallest unit of time, above the Planck time.
"Yak shaving" - A term often used by programmers to mean a chain of useless activity that is prerequisite to a desired task. Can also mean intentional non-essential procrastination.
References:
https://en.wiktionary.org/wiki/yak_shaving
http://programmers.stackexchange.com/questions/34775/correct-definition-of-the-term-yak-shaving
The line in the show could be interpreted as the team toiling away at even the most miniscule and seemingly-useless tasks to achieve tiny speed improvements.
"We're about shaving yaktoseconds off latency for every layer in the stack." -Gilfoyle