I love rail transportation, but I hate building the net manually - it's too cumbersome. So I made dis.
This mod builds a rails network at sea level (y=63) (default, configurable) in grid pattern every 16 chunks (default, configurable).
If you would like to have it Subway-style, I recommend you to set "depth" setting to 50-55, to make sure it can safely go under small lakes and in general be more safe from surface mobs.
Mod will try to avoid placing tunnels in water or lava. If there's no solid block for rails, it'll place cobblestone as a base. Every ~10 (configurable) blocks a lit pumpkin will be placed for lighting the tunnel. Also, every 11 blocks there will be booster tracks placed. Although I recommend you to use Terracart mod – it's a cart that needs no booster tracks and there's no need to carry a minecarft with you - just rightclick on tracks and you're on!
On each rails crossing there's a slab to stop your cart. If you want more complicated routing, it's up to you. If the crossing is underground, there will be a pumpkin lamp placed on top on the ground, so you can easily find it when searching for nearest track.
PS. To those who ask how tunnels are generated: if X_coord == 0 || (X_coord % (frequency * 16) == 0) then tunnel is generated at X_coord + 8, same goes for Z_coord. Depth stands for Y_coord.
Update v2:
Changed default depth to be at sea level, 63
Added beacon pumpkin on ground above crossing
Added booster tracks every 11 blocks
Increased tunnel height to be 3 blocks instead of 2 for safe dismounting without sticking your head in stone