If you have 8 DIMM slots you are fine, you can put 6 x 16GB. Everyone does their own memory upgrades, it is something designed for the end user to do. And Apple Store prices are based on 2010 price and rediculously high - DDR3 has dropped a huge amount.
MacPerformance Blog
The 2008 and later though can benefit hugely with a GTX 570 if you are in the right field.
http://forums.macrumors.com/showthread.php?p=14794775#post14794775
The 2010 can be outfitted with a pair of X5690x or 5680s too. All without having to sell and buy a new system.
Some configurations are of course Build To Order.
http://macperformanceguide.com/blog/2012/20120408_1-MacProNowOrWait.html