Confluence Server is by far the easiest application to modify visually since you can apply custom HTML Layouts and styles from within the application, without modifying source files.
It looks like the question was answered best by David Simpson of App Fusions. You should check this answer out, it's a great answer, but you should essentially:
This is the most lightweight and flexible solution. You must ensure that you 'bring' the update along when you upgrade the application.
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I should note: I haven't tested this, although I'll give it a shot at some point.
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Could you give us a screenshot so we know what Icons you're trying to replace?
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