I am partial to the the ui.r/server.r/global.r set up.
Most (all) of my apps are based on the magnificent shiny dashboard package (https://rstudio.github.io/shinydashboard/). A tip that I was told (pre-Shiny modules) was to use functions to keep the UI easy to manage (https://groups.google.com/forum/#!msg/shiny-discuss/-Ym6buKaXRU/AXna6enIOGgJ;context-place=forum/shiny-discuss) - I use this all the time!