On older acft particularly 727 and 737-200 many of those patches you saw are likely to be 'doublers' which are structurally containing/strengthening straps fitted in accordance with one of the many 'Aging Acft' Airworthiness Directives or the SSID program as the acft reaches certain age/hours or cycles - the instruction dictates the size and design of the straps/patches however some operators (mx. facilities) have done better/tidier jobs than others (or in some cases an option is to re-skin which for economic reasons an operator may not wish to do)
In the case of a 'patch' this will be down to a hole in the integral pressure hull and/or similar structural surface damage - the requirements/limits for these repairs is contained in the appropriate aircraft's 'SRM' Structural Repair Manual which dictates the size of the patch and fixing etc. dependant on where on the fuselage it is going