RAM, CPU, and expansion card upgrades
Off the top, there are RAM upgrades available from several firms, including Other World Computing, one of the most popular Mac upgrade makers. OWC currently has a 64GB RAM upgrade (16GB x 4) available for $849, significantly cheaper than the equivalent upgrade from Apple ($1,300) - OWC told me it will be launching a 128 GB RAM upgrade kit later this month.
Earlier in March, Transcend announced its own 128 GB upgrade kit priced at $2480, though Other World Computing's Larry O'Connor said his company's kit will be priced significantly lower than Transcend's offering.
Also in the works from OWC is the first Mac Pro processor upgrade program, which the firm said was possible at the beginning of January. More details will be forthcoming on that over the next week or two.
Rounding out the OWC's pro-level offerings is its Mercury Helios 2 PCIe Thunderbolt 2 expansion chassis. The $480 box allows installation of two half-length, full-height, single-width x8 PCIe cards (or one single-width and one double-width card) allowing use of expansion cards with the new Mac Pro.
External storage upgrades
LaCie is now selling its Little Big Disk Thunderbolt 2 external hard drive, offering two 500 GB PCIe solid-state drives in a RAID-0 configuration, for $1,300. According to LaCie, the drive will deliver transfer speeds up to 1,375 MB/second and up to six total Little Big Disks can be daisy-chained together for transfer speeds up to 2,600MB/s.
Cables and docking stations
For users looking to put some distance between their Mac Pro and their gear, such as audio engineers who need to have their computer and accessories in a soundproof room far away from their monitor and keyboard, Corning offers 33 and 100 foot Thunderbolt 2 cables using special optical technology. The cables aren't cheap, available for $330 and $660 respectively, but they can be safely bent or squeezed, meaning they can be run through wire channels as necessary without worry.
There are also Thunderbolt 2 docking stations in the works, including the Echo 15 Thunderbolt Dock from Sonnet that has an optional Blu-ray burner, internal hard drive bay, and a variety of different ports for legacy connectivity. Sonnet's dock is available for pre-order starting at $400, but there is no word on when it will actually ship, currently estimated at Summer 2014.
Upgrades from Apple
Finally, there are the upgrades that Apple offers on the build-to-order Mac Pro itself. iMore does a nice job explaining your choices, though there really aren't that many upgrade options aside from the CPU, the GPU, and internal solid-state storage capacity. I highly recommend however, that users purchase RAM through a third party like Other World Computing, as it is significantly cheaper than Apple's options.
The new Mac Pro is available for order from the Apple Online Store as well as third-party retailers, with orders placed today with Apple estimated to ship sometime next month.