I use Crystal Clear Acrylic from Krylon to seal the colors. You have to be careful that your sheet is flat because an accumulation of acrylic in one spot will make the counters less bright. I use several pins in the sheet and it works well for me.
http://www.krylon.com/products/crystal-clear-acrylic/
Keep in mind I don't always bother because most of the games I construct these days are playtest copies and my experience is it's more likely I will have to deface the counters myself - say because the developer changed the value during the playtest cycle - than them being damaged for lack of finish.
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I like to use 3M 77 to glue things because it gives me a second chance if I screw up.
