Less Commutes, Not Less Commuters.
Reduce the number of trips to work and you reduce traffic
As I see it, the biggest challenge with minimizing congestion is that there isn't a lot that a civic government can do with the tools available to them. The options presented are usually some variant of:
1) More public transportation (expensive, and in the case of light rail and bus lanes, requiring lots of infrastructure)
2) Congestion charges & toll lanes (burden falls disproportionately on the poor)
3) Reducing lanes and parking spots to social engineer less driving (infuriating)
However, what if the problem isn't the number of commuters, but number of commutes? Offer tax incentives for companies to shift employees to four 10-hour shifts a week instead of five 8-hour shifts. Instant 20% reduction in commutes. These 4-day shifts can be staggered to allow the business to remain open 5 days a week. Every weekend being 3 day should also play well with workers.
Furthermore, the city could incentivize telecommuting. Either from home, or perhaps from "commuting hubs" on the outskirts of the city. Facilities paid for as a joint venture between city and employers, with office amenities (high-speed internet, fax, printers, conference rooms, possibly onsite day-care to allow more mothers and fathers to remain in the workforce). There could also be food courts, reducing the need to leave for lunch.
Admittedly, these ideas aren't a magic bullet. However, they could offer some degree of congestion relief, and are (most importantly) within the powers of the city to effect.