I have two custom cards in my cube.
Deus Ex Machina: Legendary Instant, 2G. Search your library for a legendary card and put it into your hand, then shuffle. Flashback 6W.
I saw Captain Sisay and thought it would be awesome to have a legend subtheme, so I added her in. She died on the spot whenever she was played, so I designed Deus Ex Machina to do a much better job. Mostly it just fetches Thrun, but I'm making some big changes and cutting really powerful cards like Thrun. We'll see where it goes.
Corpse Caller: Creature - Human Wizard, 2B, 2/2. When Corpse caller etb, put a 2/2 zombie into play. Sacrifice a zombie: target creature gets -2/-2 until end of turn.
I was thinking a lot about black being bad in cube, and tried to fix two problems with this card. Firstly it's 4 power for 3 mana, a very good 3-dropp for black aggro, and easily castable in 2-color aggro. Secondly I always thought one of the stengths of black is cards like Nekrataal and Skinrender which lend towards grindy removal decks. Nekrataal itself just always seemed unwieldy, costing double black and having such a weak body. I wanted to make something a but more efficient, even if Corpse Caller is a little less powerful.
I designed one more card which I cut, a legendary blue creature. I think he was a 2/3 for 4UUU. He gave you reverse cascade, that is "whenever an opponent plays a spell, they reveal cards from their library until they reveal a non-land card that costs less. You may cast that card without paying its mana cost." I thought the mechanic was awesome. He hit the table once, and everybody started freaking out about how overpowered it was. In the end the guy pointed a removal spell at it and cascaded into a card I didn't actually want to cast. I took him out of the cube because I didn't think people liked seeing such a splashy effect that was not a real card. Also it was pretty swingy.
The other two cards have been fine, fun, and pretty good. My advice for designing custom cards for a cube is to do it only when you want to fill a hole. On the other hand, if the people you play with are more open to this sort of thing, design away! As many as you want! Why not? You can always cut or change stuff that doesn't work out.