electrical problem

my 99 civic ex went dead last night. It was raining, and I shut the car off to quickly run inside, and when I came back out... nothing-- just the dreaded clicking of the starter.....
I got the car jumped and it started right up.. no dummy light came on. However, I turned the radio off while I was driving, but I kept getting a clicking sound in the speakers occassionally... the same sound you might hear when you first turn on your radio and the subs click on. The clicking sound came through the speakers when I would turn on my turn signal.
Today I went out and the car is dead again. Any ideas? I haven't had any work done on the car. My subs have been in the car for years, but I disconnected all of the wiring to them just to be safe, and still the clicking remains and the interior light will flicker. I checked all the grounds, and they look fine. All fuses look good. Is there a short somewhere? Could it just be the battery?
Thanks in advance for any input... it's really driving me nuts

Do you have a meter to see what is happening with the charging system ??

Could be low voltage causing eratic operation.