3,1 upgrades
We have two of the 3,1s. Considering that most software really does not utilize the extra cores efficiently, I have always wondered why to upgrade the machine itself at all. The 3,1 is really easy to upgrade with a RAID card (we have an ARECA 1882ix), graphic cards (one of them uses a GTX 680 and the other has a GTX Titan), one has 16gb RAM and the other 32gb RAM.
The only thing that I have ever noticed making those machines go much faster was the addition of SSD drives. One of our machines uses 4 HD platters, the other has 8 1TB SSD's in a RAID 1+0 config plus two one TB SSD's connected to the ODD1 and ODD2 ports which serve as the boot drive and backup to the boot drive. Objectively, the 3,1 with all those SSDs just flies. Both machines have the latest version of OS 10.9, and I could not be happier with both of these machines.
They have served us well for the five plus years they have been in existence, and for our needs as solid servers for our office, I don't think we will dump these until Apple somehow no longer supports an upgrade path for these puppies. Until then, I am going to abuse these workhorses until the CPUs just get fried (unlikely considering they are XEON class).
That being said, we will probably buy the new MacPro trash can since it is time for some new capital expenditures.