What are the requirements for oxygen cylinder storage and the segregation of full, empty, and partial tanks?

Any examples are for illustrative purposes only. 
Storing oxygen cylinders, as per NFPA 99-2012, 11.6.5.2, is about ensuring full and empty cylinders are not comingled.  Those cylinders defined as 'empty' by the organization shall be segregated from all other cylinders that are intended for patient care use. Partials without an integral pressure gauge and those equipped with gauges with depleted volume content (as determined by the organization's policy) are to be stored with empty cylinders.

Full and partially full cylinders, as determined by organizational policy are permitted to be stored together. Empty cylinders shall be marked as such by either individual tagging, as indicated by the integral gauge (and defined by policy), or group signage, as appropriate. 

For example, if a rack containing twelve cylinders are in an area and four of the cylinders are determined to be empty, they must be segregated from the other cylinders and labeled as empty, per NFPA 99-2012, 11.6.5.2 and 11.6.5.3. If there is a separate rack designated for empty cylinders, the designation of this rack, would accomplish the “marking” of the cylinders by the nature of the rack being labeled.

Reference EC.02.05.09