The two biggest issues I always find quite difficult are:
- managing and troubleshooting (in zero-time, of course) big routing issues that involve ISDN backup and route redistribution on multiple star topology: carefully study standard metrics, and program a crash test during off-peak, to ensure everything is running.
- troubleshooting STP (and the dreaded "STP storm" when running 802.1d STP, with all network down for 50 secs, is something everybody don't want to experience in his/her network): use rapid-STP (easy, fast, reliable), or DON'T USE STP AT ALL (e.g. use Cisco "FlexLinks", or etherchannel).
These are the most common ones I've been facing, and still face.
Recently I managed to setup a new datacenter: NEVER FORGET TO LABEL ALL CABLES (and use a common labeling method/software), expecially on the ditribution switch closet.
Suggestion: use a Database where you use "circuit" to identify end-to-end connection, and "cables" to identify patches. Each cable has a parent circuit; a cicuit is made up of one or more cables (see inter-closet connection).