This is a question I've been asking myself, being broke helps make the decision for me since neither is really an option
However, I'm not thinking I'd be able to do a great job on my first time out. If you have an older case (server/firewall or whatever) lying around I figure it's worth doing a little experimenting so that when you tackle your main box, you don't screw it up.
A full workshop of tools helps, too. Let's not forget that if you have to buy tools to do decent modding, and you're not planning on modding frequently, buying pre-modded might be the ticket.
Personally, I'd find a friend that knows what they're doing and buy them a case of beer to do some nice custom stuff for me.