My site's logo had a lot of thought put into it and I'm very satisfied. Not only the symbol but every choice of color has a meaning.
The most obvious element is the command-line symbol. Of course I'm into programming and Unix, but there are a couple reasons I decide to use this symbol instead of some other computing-representing symbol, which came to my mind first.
Firstly, the minimalism. A symbol with only three simple strokes represents a general attitude I have in every area: discard everything you don't need. I actually think that that's one of the best single proverbs for life in general. In software, a simpler solution is better than a more complicated one, even if it cuts some corners; because a simpler solution has less points of failure, is easier to debug, and easier to maintain or adapt. It's good advice in storytelling and in game design too. In philosophy I place massive value on elegance and I'm always looking for ways to say that two ideas I believe in (like two virtues, or two prime emotions) are actually the same one. The more details you remove without ruining the idea, the closer you must be getting to the real concept.
The black background represents loneliness and isolation. I've talked about this briefly elsewhere, but yeah, I basically live alone. There are some other people around but I can't really talk to them about anything; the stonewalling I get is ridiculous. They won't even be honest and tell me upfront that I'm wasting my time. I even wrote the poem Solitude to vent about it. I made black the background to show that it's the most pervasive symbol.
The white underline represents philosophy and wisdom, since light gives us information. I think I first became a real philosopher when I was around 12 or 13. I started to question the catholicism I was raised with and step toward the truth that was always buried in my conscience, although I remained in denial about my apostasy until many years later, even to myself.
This might sound pompous, but I actually consider myself very wise. I think I have a vastly above average understanding of human nature (which does actually encompass all of philosophy) even among people who self-identify as philosophers.
The yellow line represents Protagonism. My favorite color has always been yellow, but by the first time I named my religion (it's been through several names), the color had already gained a religious symbolism to me. Yellow is the color of the sun, especially at dawn and dusk, and the image of a setting sun would be the Protagonist flag, if there were to be such a thing.
It's because of a couple things. Firstly, anomaly is a factor of beauty. Part of the reason all of us find the sunset colors beautiful is precisely because they're only there for that tiny sliver of the day. If the sun were yellow all day and things turned more white for a few minutes around midday, I'm sure we'd find that equally beautiful.
Secondly, I think there's something very real to the correlation between Protagonist and the sunset. More generally, it's about vast things being beautiful. I think associating beauty with vastness and faraway things leads the soul toward thinking about vast things in real life; finding a purpose other than one's own happiness. I had Rebeka allude to this in Pillars of Life, although that was before I really understood it.
The blue line represents my weakness. Water is fluid, harmless in most ways and easily appropriated. So I chose blue because I'm weak. I'm actually a pathetic social coward in real life. I'm a very bad Protagonist. But I've come to terms with that. I don't need to deny it, my wisdom prevents low self-esteem from interfering with my productivity, so I put in my logo. I even put it on top of yellow to symbolize that I'm less than halfway an ideal Protagonist.
This is part of why I want so badly to teach others, be it leading them to philosophic truth or just teaching programming or whatever. I'm not a hero. I can't fill that role. But I can fill the role of mentor. So that's the role I'll try to fill as long as I'm on team good.