Just follow everything everyone has said. And definitely read the 1st post of the 2 stickies...the CPU compatibility and the Nvidia thread. They both have lots of very useful information.
But definitely the the 1st thing you should do is the 4,1 -> 5,1 firmware update because it's 100% free. This way, whenever you want to add memory and/or update the processor, you can get the faster 1333 MHz RAM and sell the 1066 MHz that's inside it now.
But regarding the best bang for the buck, when you compare it to the current MacPro trashcan, everything is
so cheap!
For upgrading the CPUs, you can do it yourself, or find a tray swap/upgrade service on eBay...which I think it still fairly reasonably priced. To get the highest upgrade,
12 cores @ 3.46 GHz, it's $945...which will have the roughly the same CPU compute power as the $10k maxed out current MacPro trashcan.
For video cards,
you can't go wrong with MVC's flashed cards. I've been using his cards for 4 years now...a flashed GTX570 2.5 GB and currently a Titan-X. They are rock-solid. The best bang for the buck I think its the 980ti...but, the 1080 and 1070 were recently announced which are faster and cheaper...but they are not supported yet.
For SSDs, it gets a little tricky since the tower is SATA 2. You'll need a PCIe card adapter to take advent of the speed increase (or an raid card with internal lanes). One of the issue I have the MacPro tower in general is, it only has 4 PCIe slots, which fill up fast. This is where I would try to find a card that can pull double duty,
like this card. In one card, you can mount 2 2.5" SSDs, make a RAID0 and get roughly 1100 MB read/write speeds, but the card also has 2 eSATA ports for a fast external hard drive connection.
I am now realizing all of what I am saying is overkill for the average user. But if you want to make a pro level machine, the options are totally there and customizable to whatever budget you have.
