In terms of design principles, the most common implementation is to align your VLANs with your organizational structure, ie "Engineering" folks in one VLAN, Marketing in another, IP phones in another, etc. Other designs include utilizing VLAN's as "transport" of separate network functions across one (or more) cores. Layer 3 termination of VLANs ('SVI' in Cisco parlance, 'VE' in Brocade, etc) is also possible on some devices, which eliminates the need of a separate piece of hardware to do inter-VLAN communication when applicable.
VLANs become cumbersome to manage and maintain at scale, as you've probably seen cases of already on NESE. In the service provider realm, there's PB (Provider Bridging), PBB (Provider Backbone Bridging - more commonly known as "QinQ", double tagging, stacked tag, etc) and PBB-TE, the latter two have been designed to try to mitigate the limitation of a limited number of VLAN ID's that are available. There's only 12 bits available for use as a VLAN ID in a C-TAG (0x000 and 0xFFF are reserved) which is where the 4,094 limitation comes from.
VPLS and PBB-TE (MAC-in-MAC) can be used to eliminate the traditional scaling ceilings involved with PB.