1) any CAD drafting software is suitable if you can get the correct information to whomever is going to make the case for you. There are a plethora of programs for drawing out there: Solidworks($$), PTC Creo($$), AutoCAD($$) are the big players that I can recall, but there are free versions out there. Sketchup (formerly of Google?) is one of the more popular ones. But as I said, it really depends on who you are going to be getting the case made by that really will influence how and what you design.
2) Mounting holes/clips are the most important thing to consider. As for holes where LEDs, switches, connectors, etc sit, generally the PCB layout guys and enclosure developers work in tandem to get the design down pat. Making a CAD version of the important information is a good way to ensure clearances, but isn't the only way. Lucky you can get the correct distances between components in PCB software so even just a sketch on a piece of paper is a good start to ensure that you get the correct clearances as needed.
3) The only "gotcha" I can really think of is the method of which the board is mounted into the enclosure. If you are not careful you can get interference between pcb components and the case which make the board impossible to get in.
Hope this is a start for you.
-kizzap
edit: Just an afterthought that I had. Consider if you can to have the board fit in a standard, mass produced case. There are some good, professional looking cases out there, that just need a little bit of common sense style thought, which can save hours in design and get your product finished. Hell if you get big enough a lot of those manufacturers are happy to help you out with customised enclosures if it comes to it.