How do i transfer applications and bookmarks from my mac mini to a new mac mini?

Use the Migration Assistant; if run after the initial setup, it'll migrate the files and bookmarks to a different user account, or locate them or the file containing them in the Finder and move it over as you would any file.

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Monoprice.com sells an inexpensive Firewire 400 to Firewire 800 cable for transferring files between the 2 machines:

http://www.monoprice.com/products/product.asp?c_id=103&cp_id=10301&cs_id=1030105 &p_id=331&seq=1&format=1