At the beginning of episode 5, we see a flashback where Gendo drops his (clear) glasses on the ground while rescuing Rei from the entry plug after Unit 00 goes beserk. LCL spills from the entry plug and when it reaches the glasses, they break.

Rei seems to have hung onto this particular pair - in fact Shinji tries them on when he visits her apartment. But, I think Gendo probably put them back on after rescuing Rei while they were still drenched in LCL and liked the orange tint.

One of his goals throughout the series is the Human Instrumentality Project, so I think he went with an LCL-like orange tint when he got new lenses. That way, he literally sees the world through the lens of instrumentality as a constant reminder that he will see Yui again. Motivation too.

When Gendo finally achieves his goal and reunites with Yui in The End of Evangelion, we see him lying on his back. Now, his glasses look slightly tinted, but not tinted orange. He has no need to be reminded of instrumentality anymore because Yui is now finally, literally with him. But he isn't totally seeing the world clearly, as he doesn't believe he deserves love.

So far, this is a happy scene. Yui is not upset, and explains that he was avoiding Shinji. But, instrumentality is not all it's cracked up to be, and when the scene takes a somber turn the orange tint returns as Unit 01 grasps him. It seems to me that Yui had forgiven him at this point, but still has Unit 01 swallow him, because something isn't quite right. He still needs Shinji's forgiveness. So, it's a bittersweet reunion.

Then in the congratulations scene, we see Gendo and Yui together and the glasses are still tinted orange. Perhaps because Gendo has now learned that love is a process and he will continue to grow in his love for his wife, and not a destination that he simply needed to reach. And certainly, congratulating Shinji was a great step in that direction he did not do often enough without Yui there in person.

Hmm yeah the glasses are different in some instances and I never really thought that the orange tint had any significance until now. Interesting observation

Another couple places the glasses are not orange is the scene where Gendo is with Fuyutsuki seconds before Unit 01 cocks the hammer of the positron rifle. I think this is because it's right before the scene with all the bright light all over the place because of Ramiel melting away Unit 00's shield during its second shot. The artist may have simply drawn them both without orange in one sitting. Before cocking the hammer, they look frosted.

When Shinji rescues Rei from the melted entry plug, she has a vision of Gendo and his glasses are orange once again.