The phrase "five by five" is a rating of the quality of reception of a radio signal. Users of this system (most commonly used in aviation) report this information as "…x by y…" where x represents the clearness of the received signal and y represents the strength. Each variable can represent integer values between one and five with one being the lowest or weakest value and five being the highest or strongest.
"I am receiving you five by five."
"Five by five" would describe a transmission that was received with maximal clarity and strength, or "loud and clear" for the hos at home. A report of "… one by five…" would indicate strong signal strength but minimal clarity (think any adult in any Peanuts animation).
Every instance of the use of "five by five" in popular media, in my experience, has been as a phrase synonymous with "ok" and not consistent with my understanding of this system. Perhaps its use in this way is commonly accepted in general military or non-aviation circles. But more likely, I think, it is being used as generic military jargon-style window dressing. It is possible that there are other systems which use a similar format and report on different information. For example, in the classic movie Aliens Corporal Ferro, who pilots the Marine drop ship, reports that they are "…five by five." as they descend to LV-426. Clearly her system is rating the depth of the shit they are in and the likelihood that no one will survive the mission.