The best and cost effective method for Logo Printing would be Pad Printing,and if their is no colour in the logo you can even go for laser Printing but it is costly.
Computer boxes have (had) a ± 1x1 " recess on its face for a name or logo. The logo can be engraved on the back of a thin piece of transparent material (perspex) and colour filled. It is then glued on.
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