Yesterday I bought a Hercules Prophet II MX and it only has a heatsink and I was noticing that after I ran graphics hard I was getting some lockups. (Bought a open box item or I probably would have just taken it back and I wasn't really sure it was the card, cuz I added a USB mouse at the same time.) Well anyway I felt the back of the board and it was getting very hot and I haven't overclocked it yet. So I decided to see how good a connection the heatsink was making and when I took it off only the edges of where the heatsink sat had any compound on it. That cheap little blue heatsink had a major bowl in it. I took out my 330 grit and my 600 grit and lapped it down. It was bad enough I was wishing for 220 grit. Anyway the moral is that after I put it back on with some Arctic Silver my crashes stopped completely. So if your heatsink is making very poor contact it will help alot but if you just have a few scratches then thermal compound usually does a good enough job that lapping doesn't give a major improvement.
Like the otehrs said, it varies a lot. My idea on it, is that you might as well, since it costs about $.50 for the sand-paper, and then you know for sure it's the best you can do.
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