Ok, here's a question from the long-out-of-town:

In San Francisco and Silicon Valley, the Caltrain runs with a bicycle car that accomodates 24 bicycles per trip (sometimes two cars at rush hour, because they fill up fast). Bikes are allowed on the BART (SF/Oakland/Berkeley) lines during off-peak hours.

In New York, you can take your bicycle on the subways 24/7.

When I was in Philly, I remember "up to two" off-peak bicycles on the subways, and also on the regional rail lines. For this you had to have a $10/year pass from SEPTA. (When I was working out past the main line, I reverse-commuted with my bike on the R5 - out from 30th Street in the morning, in from Paoli in the evenings. mostly, I took it to Norristown a lot on the weekends to visit friends by King o' Pressure.)

Has the bikes-on-transit situation improved any in Philly? Are they putting any racks on the buses? Allowing more bikes or more hours on the trains?

According to SEPTA's website, you no longer need a permit. You can bring your bike during off-peak hours (9a-3p and after 6p) and on holidays and weekends, and SEPTA allows two bikes per car. I haven't seen any racks on the buses, but some stations have racks. Bryn Mawr, Wayne, and Fox Chase have bike lockers you can rent.