It's important to never allow your battery to get this low in the first place. Fully discharging Li-Ion and Li-Po batteries can damage the materials inside them and make them unable to absorb a charge again. If your battery has been fully discharged, it will almost certainly take the AC charger and a LOT longer than usual to recharge it, if it can hold a charge at all. If it hasn't gone above 1% after 24 hours on the AC charger, it is dead. Try to never let it fall below 5%.
Have you tried a power management app like JuiceDefender? I was a bit skeptical, but installing the Ultimate version and tweaking the schedule and triggers so that the data services were turned on and apps allowed to check for updates only periodically drastically improved my battery life (and boosted my productivity, since I wasn't constantly checking my new email!). I went from 8 hours full-to-dead to still having 50% charge at the end of the day. It's set to automatically turn on data connectivity whenever I launch an application that needs it (browser, email, etc) so at worst there is a ~2 second delay while I wait for the connection to establish.
It gets the best savings with Root permissions which allows you to set CPU speeds for min, idle, and max power, but since you are running CyanogenMod, I doubt that you'll have any problem with that.