Copy Files to new iMac and fresh install of Apps?

I am upgrading to a new 27" iMac from a Mid (2007) 24" Core 2 Duo
My understanding is that setup assistant or migration assistant, will copy over my user data, applications, etc....  My issue is, I don't want a lot of that copied over to the new machine.  For instance, If I understand correctly, if I copy the Apps, it is an all or nothing scenario, correct? 
Would I be better off just setting up the new iMac "as-is" out of the box, and just reinstall the apps that I want?
Also, for my user directory, couldn't I just copy those files off to an external hard drive from the old machine, and copy them back into the new one?

With a new Mac running Mountain Lion, I would install the latest (newest) versions of all apps from scratch.  I would not migrate apps from an older system.  You said your existing Mac is a 2007 iMac - what version of OS X are you using?
You can easily transfer all your data files (things that are in your old user folder and elsewhere on your old Mac by starting it in Target Disk Mode and connecting it via FW to your new Mac.  Then just user the FInder to copy whatever files/folders you want to transfer to your new iMac. There is no need to do a "double copy" by copying them to an external drive first, and then copying them a second time from the external drive to your new iMac.
Note: you will probably need the Apple Thunderbolt-Firewire Adapter to do this.

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