Gee, I wish I had 12 Vipers, then I'll do TnRs with them or flick them out of the window (ok ok don't flame me, I'm kidding).
Actually I think the Custom cards started because of all the different finishes that are applied to the cards. If you're talking about design my personal opinion is that it doesn't really... qualify as a custom card because there's a hundred and one designs out there. Someone must have realized after some time that XYZ brand card doesn't fan very well and its hard to perform, so he decided to find a new kind of finish, chuck it on the card, and sell it for a dang load of moolah. And well, us being the hardcore magicians happily go "ooh, ahhh, that's da bomb!" and buy it. Not that its bad, but well, its human psychology.
Coming to think about it, the good thing about Custom cards is that they really garner attention, which is needed sometimes. Walk into a bar and take out a black deck (I shall attempt to avoid brands/names) with some shiny designs and people will go "Hey, where'd you get those cards?" For people who have difficulty breaking the ice when trying to perform magic, that's a great option. But at the same time, there's also the problem that people get suspicious of custom decks because they look totally different. I've had a guy come up to me before and ask to examine my deck because it didn't look like a Bike.
Personally, my entry to the flourishing scene in my place was catalyzed by the existence of these custom decks. I mean look, the first time I tried flourishing I had to contend with a free deck from an Airline, and those were pieces of cardboard. Literally. Then I went and got a black deck and I found the cards feeling like silk and I got hooked. Now after flourishing for a year I find I'm reverting back to TH9s and Bikes because my skill has improved.