I just purchased a new MacPro to replace my existing 2006 MacPro which cannot be undated with the new operating system.  My question is what is the safest way to transfer all my files.  1) simply install my existing 2TB HD into the new Mac Pro or 2)

I just purchased a new MacPro 3.2GHz Quad-Core Intel Xeon processor to replace my existing 2006 MacPro 2 x 2.66 GHz Dual-Core Intel Xeon because it cannot be undated with the new Lion operating system.
My question is what is the safest way to transfer all my files to the new computer.  1) simply install my existing 2TB HD into the new Mac Pro, set it as the startup drive, and update its10.7  operating system or 2) or use the migration program.
I'm concerned that simply installing the existing 2TB HD, I may have issues with it not recognising some infromation written for the old 2 x 2.66 GHz Dual-Core Intel Xeon.

your new system runs 10.6.8 just fine as has been said and stated many times.
I would clone it first.
I would even clone the original system it has.
And if you have or want to use Lion and then Mountain Lion, fine - I would still keep backups of every OS.
I am not a fan of putting the OS and Apps plus all the data all on one drive. I like to keep them separate.
Whatever OS, rerun the last combo update is all and any other updates.
And by "new Lion" I assume you don't mean 10.7 but "Moutain" 10.8.  Part of me says keep Lion and SL around, and test and try out ML with your apps and other hardware you may have. After too many years, waiting for 10.8.1 - and give everyone time to update their apps and retest.

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