PCGen will save to a stat block format, but the only other free software that I can remember is for 3.0, and even that is no longer available where it used to be.
It could be serviceable for 3.5 if you are willing to go in and change the monster entries to the correct 3.5 information. It would be missing some of the fields from 3.5 like the Base Attack/Grapple field and Full Attack field (it only has "Attack") but you might be able to work around that. It is pretty easy to use and I don't recall many bugs. I hope they decide to update it since it does exactly what I need: gives me the ability to enter information in an "easy to enter" format and rearranges that information into a statblock.
Another program called Monster 3.5 will output a statblock in HTML format. I don't think you can enter information into this program but it has the 3.5 fields and monsters from the SRD.