I had converted several hundreds flv video to mpg using ffmpeg.
The screen resolution of the flv and mpg files are exactly the
same (ie 320x240 pixel).

Everything is OK, only in several video, the result is
"Pixelated" or small squares appear on the picture.

Is it possible to change ffmpeg parameters to reduce / eliminate
this "pixelated" effect?

It all depends on what codec you are using etc...

Post the ffmpeg command that you used and we can probably give you a better idea of what to do, but here are a couple of ideas:

-try using a different codec (xvid maybe? - do you *need* the output video to be mpg?)
-try increasing the bit rate (use "-b XXXk" where XXX is your desired bitrate in kbps)
-try multiple pass encoding, run the same command twice, the first time with the "-pass 1" option and the second time with the "-pass 2" option
-try blurring the video a bit with "-qblur XXX" where XXX is some number (try values between 0.3-1.0)

I've had this problem again and again, and I finally had to reverse engineer a video that I had seen transcoded properly. Its bit rate was around 2572k. So I took my audio and video streams and muxed them with the command below. The pixellation finally disappeared.

Hope this helps you or someone, because I know what an annoyance that problem is.