Shapeoko upgrades can be categorized into four major categories:
- those which increase stiffness / rigidity
- those which increase working area
- different spindle choices
- those which are for user convenience / other
The eShapeOko (European / Extended) marketed by cvoinescu includes a number of upgrades by default as well as a number of options at order time.
The ShapeOko 3 has been announced and is an all-new machine design which obviates the need for most upgrades and makes expanding the machine much simpler.
The importance of improving this cannot be understated as noted in forum discussion: Re: spindle power / feed rate.
User cvoinescu made an initial codification of the effect of upgrades on stiffness / rigidity in the forum thread Custom Plates. In order of effectiveness of the modifications (from most effective to least):
- Dual Y drive (either Drive Shaft or Dual Motor)
- Double Makerslide X-Axis --- shapeoko_upgrade_parts_v3.zip
- X carriage reinforced with, say, extrusion between the two plates, instead of relying only on the X wheel bolts
- the two X rails 20-30mm apart and rigidly coupled together, e.g. sandwiching between them some standard extrusion and bolted together along the length
- Moving the Z wheels further apart, i.e. replacing the standard plate with a taller one
- (for a long machine) Mid-span supports for the Y rails, and/or doubling it with standard extrusion bolted along the length --- two supports evenly spaced for each side optimal. c.f. http://www.improbableconstruct.com/collections/upgrades/products/shapeoko-2-mid-span-support
- Moving the Z leadscrew to the side to reduce the length (and hence flex) of the Z wheel bolts
- Thicker plates
There is some uncertainty about the order of the last two items on the list.
With the Shapeoko 2 already having many upgrades in place already, the priority shifts a bit --- best rigidity mods for SO2?:
- bolting X-axis Makerslide together
- mount spindle closer
One straight-forward and inexpensive way to improve rigidity is to replace the nylon spacers. There are several options.
"Biggest bang for the buck."
Now standard on the Shapeoko 2. Forum discussion in We should switch to metal spacers.
A 10-pack of 1/4" spacers should fit out a machine w/ Double Makerslide X-Axis --- 6 1" spacers (and some washers) will properly space the carriage (drilling 2 additional holes in the Z-axis mount plate will let one use 2 additional bolts and 4 more 1" spacers to finish off a 10-pack and further improve a machine's rigidity).
Alternately, user wlanfox used plastic blocks instead of spacers as shown in the forum post Shapeoko #0735, mods evolution... (at least my version) ;-)
A third option is to use (locking) nuts in lieu of the spacers as danimal documented in Re: Why not a wider "double X-axis"?
There is now a hard-coated Makerslide alternative, Openrail, which in theory affords the usage of steel wheels (in practice, not so much). Forum user microwavesafe took advantage of this for his machine as documented in X and Z mods.
Note that they are most useful for the X- and Z-axes: Re: Metal Dual V wheel And Fishing line pulley Bearing and Re: Hardcoat OpenRail.
Double X-carriage motor mount plates
Another option which needs to be fitted into the above is doubling up the motor mounting plates for the X/Z plate assembly and increasing the number of bolts used so as to create more rigid torsion box as the eShapeoko does (though its is also taller) --- this upgrade has since become standard in the ShapeOko 2.
The Double Makerslide X-Axis upgrade is the primary way to address this. Now standard on the Shapeoko 2.
A similar idea to increase the rigidity of the gantry is shown in Bar across the back...
- fasten the two lengths of rail together --- bolt, screw, epoxy or use the Makerslide joining clips
- sister in length(s) of steel along the top or bottom or in-between
- fashion some sort of plates to join the pieces of Makerslide together
Furthering this idea, Xaracen extended the V-wheel bolts for his Z-axis through his gantry on his SO1 by drilling matching holes, using longer bolts and appropriate spacers. http://www.shapeoko.com/forum/viewtopic.php?f=11&t=3734&p=37129#p37126
Yet another option is to add additional sets of wheels mounted to a secondary carriage as done on Marty's Shapeoko2 Deluxe.
These upgrades are easily compared and complementary in nature, see the page Scaling Up.
Often, other minor upgrades can affect this, e.g., moving belts to the outside as documented in some of the methods shown on the Belt Anchors page, or Belt on outside, but it is also possible to lose working area as when doubling the X-axis Makerslide.
Open End Plates
One elegant solution is the Open End Plates, which allow one to extend a machine along the X-axis more readily. Now standard on the Shapeoko 2.
Another alternative is to use aluminum extrusion itself for the frame as forum user Juicebox did in Just Enlarged my Shapeoko with some UpGrades.
Spindles / Tooling
Rotary Spindle Options
Note that spindles may be upgraded w/ better collets. Some are merely replacements for the standard collets in different sizes, while at least one manufacturer offers specialized systems which allow one to use ER style collets. These are more convenient and easier to change (esp. if one buys a matching nut for each collet) and afford a greater clamping tolerance (e.g., a 1/4" collet can hold a 6mm endmill).
Similar to a rotary spindle is a high-speed engraving tool:
- holder for Roland vinyl cutting knife on Thingiverse
- plotted vinyl
- vinyl_knife_holder.dxf cchristianson's Google drive
- Re: Vinyl Cutting Blade
- Silhouette craft cutter: GPGL Reference, Courtesy of Graphtec 
- CNCZone: Drag Knife for CNC [Pics+Video]
- Thingiverse: 3D Printer Cutter Tool
- 3D printed: http://www.shapeoko.com/forum/viewtopic.php?f=24&t=6335
Pick and Place
- First test of my ShapeOko pick and place prototype
- Shapeoko and Pick and Place
- ACME Z-axis --- see also A new Z-axis nut - metal on metal w/ built in anti-backlash and Modified Z drive Assembly --- this upgrade is especially of interest to help overcome Grbl's limit that all axes must have the same acceleration.
- Possible New Z Axis Design for the ShapeOko (1)
- Belt Anchors
- Touch Probe --- plans and software for constructing one here: http://www.vinland.com/Touch-Probe.html
- Cable Management
- Dust collection
- Emergency Stop (E-Stop)
- Enclosures --- an enclosure of some kind, either for the electronics, or the machine is essential if cutting metal, so as to protect the electronics from conductive chips.
- Headless --- adding a second Arduino and SD-card shield to allow headless operation
- Limit (Home) Switches --- c.f., linear encoders: http://www.directindustry.com/industrial-manufacturer/linear-encoder-65005.html 
- Nio's V slot bed
- Y-Axis Wheel Covers --- includes mount for cotton swab for cleaning.
- Coolant System --- manual application of coolant is deprecated since it may cause thermal shock to the tool.
- X/Z Axis Plates Smaller plates for holding the X-axis motor and the whole Z-axis assembly.
- Pulley Drive system 4:1
- Shapeoko Z-Knob --- .svg source
- Under-Rail Lighting
- Touch Plate --- see the Limit switch page.
- Fourth Axis
- Shapeoko 3 https://plus.google.com/100117868275643909021/posts/BUcEXpQjzQp 
- Fifth Axis --- One could in theory just purchase an accessory table and bolt it to the bed of one's machine.
GrblGru now supports lathe functionality: http://www.shapeoko.com/forum/viewtopic.php?f=6&t=4710&p=42654
NEMA 23 motors
Upgrading the motors is usually done to:
- move the machine faster
- move a large, heavy spindle
there's no intrinsic reason to upgrade from NEMA17 motors.
Documented for the ShapeOko 2 in this forum post: Re: Caleb's Shapeoko 2 #3164. NEMA 23 Z-axis for shapeoko 2. Note that these may need longer fasteners --- 15mm per . It will also be necessary to source pulleys with a 1/4" bore (as opposed to the typical 5mm of NEMA 17 motors). A larger plate is needed for the Z-Axis and is available from I.C. on the Upgrades page --- NEMA 23 Z-Axis Kit.
- Nema23 on Z-Axis --- includes plans for mount plates. PDF file here: Re: Nema 23 Z Axis Plate and a link to Thingiverse.
- Shapeoko 2 Kit Mechanical Kit with Nema 23 --- project on Inventables.
Notes on motor selection size: You don't want a motor heavier than about 700 g, mostly because there's absolutely no point to it. Why would you want to be able to apply, say, 600 N to the gantry or X carriage, when you know that 100 N on your tool will flex the machine too much to be usable?
Z-axis Drive options
For the Z-axis, rather than directly driving the threaded/Acme rod, it's possible to use a belt drive:
Discussion here: http://www.shapeoko.com/forum/viewtopic.php?f=12&t=4368 and source files are available in this post: http://www.shapeoko.com/forum/viewtopic.php?f=12&t=4368&p=33383
- shapeoko.com --- Acme Z-Axis, NEMA 23 Z-Axis, DW660 Mounts, DW660 Dust Shoe, Z-axis belt drive
- Inventables --- parts, dual drive kit, open end plate, motor mount plate
- Kbot3D --- 3D printed upgrade parts including: DW660 Vacuum Attachment/Dust Shoe, Lift Blocks, CNC Table Clamps
- Amber Spyglass Ltd --- parts, open end plates
- Reactive Storefront --- Precision V-Wheel Spacers
- Donek Tools --- Drag Knife for CNC Routers