Can anybody tell me In what way I can have h.264 output in after effects?. This feature is not available in format. I am utilizing Adobe CS4. 
Hi there,
Composition -> Add to render queue -> Click on the “Output module” -> In format choose Quicktime Movie -> Click on the format options (pop up will open) -> and in compression type choose h.264!
If it not helps and shows error then you should use the format box on top in the LOSSLESS BOX and select H264 from there. Then you will get the H264 options window.
I hope it helped.