The Shapeoko is a great machine out of the box, and there is really no need to modify it to get good results. No, really, check out Winston Moy's videos if you need convincing. Still, once you are reasonably comfortable with the machine, and how to set optimal CAD/CAM parameters, chances are you may be tempted to optimize the machine itself.
There are many possible hardware upgrades. Some are cheap, some are definitely expensive: this section provides a brief overview of the popular ones. Whether they add enough value for money is highly debatable, and completely depends on your use cases.
The standard limit switches are fine, but they have mechanical parts that can wear out over time and eventually fail, which would result in a machine crash when homing. But the main reason to upgrade is to get an (even) better precision/repeatability when homing.
Contactless/proximity switches trigger when a metal object comes within a certain distance of their surface. Since there is no mechanical contact with the moving part, there is no mechanical wearout, and they also happen to be more precise. Here's an example of a proximity switch for the Z-axis:
They can be used as an (almost) drop-in replacement for the original switches, the only difference is that (depending on their technology) they may need an additional lead for power supply, connected to one power pin of the controller board (typically, the 5V pin on the Arduino ISP header, see Anatomy of a Shapeoko for details).
Probably the most popular upgrade is the replacing the stock X/Z carriage with a sturdier one. This is by nature a costly upgrade since it involves multiple large metal parts, linear rails, and a likely ball screw. A few reasons to consider this upgrade path are:
to eliminate the chances of the Z-belt slipping on the pulley when improperly tensioned.
to eliminate the intrinsic (small) front/back slop of the original design, between the main Z-plate and the sliding plate.
to support the weight of a spindle, that is typically much heavier than a router. Additional springs can be added as an alternative.
Here's an example of the Heavy Duty Z upgrade on my machine:
There are two main reasons to replace the original MDF bed:
to match a specific workholding solution (e.g. T-tracks)
to make the Shapeoko more rigid.
While the T-tracks bed upgrade (that comes as an alternative to the "sea of holes" wasteboard) typically still uses MDF strips, upgrading to an aluminium bed is a good albeit expensive way to improve machine rigidity as well as have a more "weather-insensitive" machine (MDF tends to absorb humidity, which may lead to some warping/swelling over time)
This one is 12mm / ~0.5", the one on Carbide3D's store is 0.5" thick too.
This is probably the cheapest upgrade: replacing the original GT2 belts with reinforced ones. The two most popular are steel-core belts, and kevlar belts.
Here's a section view of steel-core belts showing the embedded steel wires:
Buying several meters of steel-core belts is cheap, will serve as a provision in case the original belts snap, and replacing the belts is very easy (since it does not involve disassembling anything else that the belt tensioners) so that upgrade is a no brainer if you feel you can benefit from the increased robustness, and possibly from the ability to push the max speed and acceleration beyond the default settings:
Having to manually set RPMs on the router knob at the beginning of each job can get old, and is also error prone. Luckily the Shapeoko controller board happens to have a "PWM" output that GRBL modulates as a function of the RPM values found in the G-code. So it is possible to feed this signal into a dedicated power controller, that will adjust the voltage applied on the router power leads accordingly, resulting in a specific RPM value.
This requires buying such a power control module, the most popular one is the SuperPID. You need to know what you are doing since installing it requires wiring mains.
Beyond the automatic RPM control, the added benefit is that this allows the router to operate at a lower RPM value than the minimal knob setting, e.g. to run at 5000 RPM on a Makita that normally mins out at 10.000RPM.
The Shapeoko uses a trim router by default for cost/convenience reasons, but all higher-end CNCs use a spindle instead. Some of the main benefits are:
a spindle can run at lower RPMs than a router (some models can run at much higher max RPMs too), and usually has higher torque. Since a spindle needs a dedicated controller to run anyway, the automatic RPM control described above is a given.
the runout is smaller.
it is WAY quieter than a router.
there is no need to change bushing, so basically no maintenance.
it usually supports "ER" collets, which come in much more varied sizes than trim router collets.
They come in two types: air-cooled and water-cooled (you then need to add a water tank & pump in the setup), and at various power ratings, the most popular being 1.5kW and 2.2kW.
They are significantly heavier than a router, so this upgrade is often associated with a ball screw Z axis upgrade. An 800W spindle can therefore be a very interesting option too, to get most of the benefits without the need to adapt the Z-axis to cope with the extra weight, and it's cheaper too.
Installation will require wiring the PWM signal from the Shapeoko controller board to the spindle controller. The wiring/configuration of the spindle controller itself may not be a piece of cake, depending on the available documentation (spoiler alert: chances are you will buy your spindle kit from China, documentation will be sub-par, but the community is here to sort it out).
This goes beyond the topic of CNC, but for folks who are considering getting a laser cutter the opportunity to use the Shapeoko instead of buying/building a standalone machine is right there, it boils down to:
attaching a laser module somewhere on the X/Z plate, often on the router mount.
wiring the PWM signal from the controller board to the laser module, to allow modulation of the laser from G-code.
using a specific software to generate G-code for the laser job.
It seems to me that the mininum one should do to use a laser module safely is:
have the laser power interlocked with the presence of whatever physical protection/cover you are using: it must be impossible for power to get to the laser (voluntarily or by accident) if the protection is not present.
wear proper laser goggles at all times as soon as the thing is POTENTIALLY turned on (that includes moments when the power if off, but under the control of the machine i.e. the G-code/controller). Never, ever trust a single element of software or hardware alone to keep you safe.
stay by the machine while it is running. Seriously, don't burn down your house for a laser cut gone wrong.
On top of that, you should also have proper ventilation in the room, and possibly a fume extraction system, which will result in much better laser cuts quality anyway !