For modern high bypass commercial engines with large diameter fans and high pressure ratios, a three spool configuration is worth the added cost and complexity over a conventional two spool in terms of efficiency.
As turbofan engines get smaller, packaging three shafts can get difficult. The innermost shaft coupling the fan and LP turbine has the smallest diameter, longest length, and transfers the most torque.
The best solution for large commercial applications presently seems to be two spools plus a geared fan, like Pratt's GTF. Stepping the shaft speed down between the LPC/LPT spool and fan allows each to be more highly optimized. The diameter/speeds of the LPC/LPT are no longer compromised to accommodate large fans, which also allows fewer stages.
Rolls-Royce plans to combine their three spool configuration with a geared fan for their future Ultrafan Engine.
This slide shows a comparison between their advanced three spool engine and their Ultrafan engine with a geared fan. Notice how much smaller the diameter of the LPT section is on the Ultrafan engine.