September information is now up.
Pacific Surfliner +0.8% (-5% for year)
Capitol Corridor -8.9% (+2% for year)
San Joaquin +7.8% (+7% for year)
Coast Starlight +7.8%
Pacific Surfliner +8.2% (+6% for year)
Capitol Corridor +3.5%
San Joaquin +3.0%
Coast Starlight +0.8%
Impressively, on time performance for the Surfliner Express hit 100% in September, in large part thanks to a new equipment rotation which results in it using single level equipment only every other day. Overall the Surfliner has vastly improved its OTP with 84.6% for September; though this is with a more lenient standard than the commuter rail agencies. Coaster maintained an impressive 99.1% OTP while Metrolink's Ventura and Orange County lines were 98.0% and 96.2% respectively.
One factor for the decline in commuter ridership was the loss of two weekdays in September 2012 compared to the year prior. Coaster the Surfliner were both affected by the shutdown of track south of Oceanside for one weekend though this did not prevent the Surfliner from managing to increase ridership mildly.
The Capitol Corridor and Starlight present an interesting set of contrasts when it comes to revenue and ridership. A tremendously steep decline in ridership, likely in part for the same reason as the commuter rail agencies, still results in a fairly decent increase in revenue while the Starlight, despite nearly doubling the national growth rate, eked out a miserly increase in revenue that won't even hold up with inflation. I'm honestly not sure how the Starlight in particular managed to do that. Presumably the ridership increase is from using it for short distance trips that do not yield very much, but there's no station pair information available.
One further interesting note is the mention that the Coast Daylight "should ideally continue on to San Diego." Hopefully the northern end will see an extension to Sacramento as well for a one-seat ride through most of California's major metropolitan areas.