I like this thread, I wish we did more community-building stuff like this.
My favorite cards? Damn, I don't know, I've made a LOT of cards, and there was that stretch of a couple months where I felt I could do no wrong, especially in red (I have a stretch of like ten red cards in a row in the master list, when no one was doing red cards).
Yawgmoth's Whim is still my favorite black card of all. It has so many deep ramifications - it gives a huge boost to people without power cards who are forced to play againt some jerk who gets Lotus and Ancestral and Walk all the time. It also punishes the over-proliferation of artifacts.
I really like Entropy, which was kind of a Matt/Bram collaboration. It seems like just the sort of card a lot of casual or theme black decks could want.
I really thought my creature-type cards (Desecrate, Domesticate, Convert, Recruit, and Enlighten) were really cool but they got like two replies in two weeks, so I guess not many other people were on that boat.
Faces in the Dark was great, I thought. THAT one sparked a lot of controversy, which was nice.
Dread Portal I will mention because I think that too often we just remake an existing card. Portal is one of my most innovative cards, and it feels very black - there's this doorway to another world, and you don't know WHAT's going to come out of it, but you know it's not going to be pleasant!
Many-Tentacled Thing was just one of my moments of pure inspiration. I was sitting at my mom's house, just reading a newspaper or magazine, when the image of this writhing black mass reaching out its tentacles and strangling a band of warriors came to me. I wrote down the card exactly as it made it into the list about three seconds later, and there it was.
Moving on to blue, I really liked Astrologer, because it's the kind of ability you can tell could be really useful sometimes, but isn't particularly broken.
Irridescent Avizoa wasn't my card, but it does feature some of my best flavor text. Same goes for Blood Elemental. Spark Elemental HAD good flavor text, but since Wizards stole my name, I've had to rename it to something awful, I don't even remember what.
Treetop Observatory was my only really great green card. Watched Grove had some powerful flavor text, though, for those who remember Yawgmoth's Edict.
Diversionary Ruse, Concealed Explosives, and Contumacy all explored some lesser-seen mechanics of red, while still being totally in-color. Change of Fortune is one I like too, because it so perfectly simulates the old mulligan rules.
I really like how Null Moon's flavor text complements its ability while not being so lame as to directly describe that ability. More flavor texts should work like that.
Watchful Sentry: I like this one because I just plain like gargoyles. I made this one in homage to one of the better stories in the second Harperback Magic anthology.
Argivian Archaeology looks so fun. I like cards like this, that show such promise. I'm sure most of my cards would be used and used well in some casual deck, yet would still be intriguing enough to be tournament-worthy.
Forbidden Plane: I don't know if anyone has noticed, but I've been pushing an enchant world theme to our cards for a long, long time - ever since the beginning, really. Even to the extent of suggesting other people's cards be made into EWs. Unlike the idea of a legendary card, EWs work
against the luck of the draw: if a legend is really good (like Lin Sivvi was), games can be decided based on who drew it first. The opposite is true of EWs.
Recant is, I think, the kind of card that should become a STAPLE for white in the same sense that Shock is a staple for red. It's totally in-flavor, effect matches ability...it even has that white feel where it never is what it it looks like. Geddon LOOKS symmetrical, but really isn't; this looks like a counterspell (or doesn't, depending on how you look at it) but it really it isn't (or is).
Watchman's Emblem: I've always liked the idea of having Wizards have certain wards and enchantments and glamours about themselves, and it's somethig you see a lot in fantasy, yet very few cards actually represent those kind of spells.
I like Pain Elemental a lot. I thought this one up while swimming. Even touching him causes pain, and the harder you swing, the more it hurts.
White Lotus: nice staple card, like Lotus Petal. Pretty un-broken for a free three mana.
Ingenuity: I really liked the incarnations. Notice that both this and Vitaility are cumulative, which is something none of the others do.
Catalyzing Agent: I really like cards that require cards to be named. I also really like multipurpose cards. This one has both, and for a price that's actually playable.
Speaking of incarnations, they were the reason I wanted to see Moonlit Landscape see print. Now I can actually reap the benefits without having to buy dual lands!
-If there was one card of yours that you could remove from the master list, what would it be and why?
Well, I CAN remove my cards from the master list

Honestly though, the one that scares me the most is Aneurysm. I get a creeping feeling everytime I see it that it's another Upheaval waiting to happen.
The only other contender is Royal Circlet, because I can imagine that being absolutely devastating in multiplayer. However, so was Mind's Eye, and at the same cost, so that assuages my worries.
Gerrymander: I'm disappointed you didn't mention my favorite card of yours: Gargoyle Eyes! That card was
awesome.