Portal onion routing
See basic information about Portals.
Portal Onion Routing is a secure way to link a secure location with an insecure location, such as linking your secure main base with spawn, or with some other compromised area. It's generally understood that direct links are far too risky, no matter well hidden the portal is. Portal Onion Routing offers an acceptable trade-off between security and convenience, at the cost of greater number of diamond blocks for more portals.
Example
As depicted in the example, the base is connected to spawn through "chains", or "waypoints". The player uses each chain and proceeds to the secret coordinates to the next chain. Using this method, you can ensure that as long as the last waypoint is not discovered (the last link in the chain), your base will remain secure.
Possible Pitfalls
This method is not fool-proof. It is slightly less secure than having no route at all, however if done correctly, should only prove to be a small loss of security in exchange for a huge gain in convenience. One must be careful of these pitfalls:
Someone could follow you while invisible, discovering the waypoints you used Your waypoints aren't hidden well enough There aren't enough waypoints, leading to reduced security