The only reason I went custom was I get 20% off them. They are still a bit spendy but I also had to spend a certain amount to get my full insurance payment and not wanting a carbon mountain bike meant I needed to spend about $1k more to hit it. So I understand they are not for everyone.
Depending on what you have now you can get some wheels that will be a huge upgrade without dropping a lot of money. Might want to start watching towards the summer if you can wait for the next year models to drop and then you can find great deals on this year's wheels. That is what DH did when he got some upgrades for his mountain bike.
You can always keep your wheels and sell the stock ones if you replace the bike.
Amanda
2011 Specialized Epic Comp 29er | Specialized Phenom | "Marie Laveau"
2007 Cannondale Synapse Carbon Road | Selle Italia Lady Gel Flow | "Miranda"
You don't have to be great to get started, but you do have to get started to be great. -Lee J. Colan