I have been having an issue the last few days and finally figured it out. Every time I opened Synaptic and selected Settings>>Repositories my laptop would just freeze up. It would sometimes stop and start slowly. I could see in the panel, the cpu usage was not getting pinned(when it would actually be moving). I was able, a couple times, to get to VT2 and log in, run top and see that synaptic was using 85-90% of my memory(4Gig). After some poking around I found /etc/apt/sources.list was huge, 156mb with thousands of lines with just ###### over and over again. I took it out of the equation and everything returned to normal. I assume Synaptic was just trying to read the file.
Has anyone seen this? Any idea where it would have come from?