Two clarifications
This is not a post about which 3D printer you should purchase, though here’s a great analysis on the subject. This post is dedicated to discussing the difference in materials when using hobby and commercial 3D printers, and how it may influence your design.

Next, the 3D printing processes Fused Filament Fabrication (FFF) and Fused Deposition Modeling (FDM) are basically the same (FDM is a Stratasys trademark). To show how similar they are, here’s a scale model jet turbine made via a RepRap machine compared to a full-scale model turbo prop made via a Stratasys machine. Both processes do a solid job at rapid prototyping, but there are some important nuances that should be considered when designing your parts. That distinction primarily involves deciding whether a hobby-level 3D printer is suitable for a project vs. a commercial-grade printer. We explore the differences here.

Both are great, with limitations
Hobby-level is great for

Cheap prototyping Seriously, at about $0.03 per gram, this is as cheap as it gets.
Fast printing Want something in your hand as fast as possible? Set a large layer height and watch your printer fly. You can also have greater control over the infill of your print, which means you can lay down the least amount of material necessary to keep your model from collapsing in on itself.
Experimentation Want to 3D print in chocolate? Go for it! Want to quickly switch between PLA, ABS, and PC? Not a problem. Cheap machines are awesome for this, and if you destroy an extruder or mangle one of your stepper motors, spare parts are readily available.
Hobby-level is not great for

Mechanical performance Delamination is a chief concern when printing from a hobby-level machine. Here’s a great example of what that can look like. In case anyone is currently experiencing delamination woes, 3ders posted some handy tips for mitigating this problem (pulled from a thorough discussion on Soliforum).
Consistency One of the tradeoffs made in low cost filament is consistency in cross sectional area. Ideally, if you look at 3D printing filament head-on it should be a circle, but along a stretch of filament the cross section can change from a circle to an oval, which can affect the quality of the print. Protoparadigm has an incredibly thorough rundown of exactly what this looks like and how you can take measures to lessen its effect on prints.
Support Material Ask someone who regularly prints using a hobby-level machine how much support material they use. Their answer will likely be “as little as possible”. Yes, dual extruder machines are making progress with utilizing support material alongside structure material, but right now the vast majority of hobby-level printers simply use structure material (PLA, ABS, etc) for their support. Since the structure and support materials are the same, removal is tedious and the surface finish suffers (though post processing with acetone vapor is an increasingly viable option). If you can design your parts without any need for support material then great, but if that’s not possible and surface finish is important, you’re better off using a commercial-grade printer.
Commercial-grade is great for

Mechanical performance These are some of the strongest plastic 3D printing parts you’ll get. In the datasheets found later in this post, you can see that hobby-level ABS has a tensile strength of about half that of Ultem (a commercial-level material).
Consistency Heated build chambers mean a lot less warping, which if you’ve talked to anyone printing ABS on a RepRap machine, is challenge that often needs addressing. There are some interesting solutions out there, but the commercial solution is to use a heated build chamber, which allows for the entire part to be printed before letting the thermoplastic cool down to room temperature.
Production use In certain production cases, having certified parts can be crucial. For instance, one of the great properties of Ultem is that it’s flame retardant, which allows it to be certified for use in aircraft.

Support Material The right-hand picture at the top of this post is a part printed using soluble support material to accomodate for the overhangs and undercuts present in the model. Since the material is soluble there are virtually no signs of the support material once it’s been removed. Awesome.

Large geometries Build envelopes can go as large as 914 x 610 x 914 mm, as this video shows (I’m ignoring 3D printing for architecture applications since it’s worthy of an entirely separate discussion). Remember the Urbee? It was printed using commercial-level printers. If you need to print prototype cars, then this is likely how you’re going to do it (however, I will add that Gigabot recently finished a successful Kickstarter for a 600mm x 600mm x 600mm FFF printer).
Commercial-grade is not great for

Quick and dirty printing You’re not going to beat hobby-level printers if you’re looking for quick and dirty prints (which is fantastic if you’re iterating quickly). Even if you use non-OEM vendors, material is still going to cost you between $0.20 – $0.25 per gram. Not quite a magnitude more expensive than hobby filament, but enough to make you reconsider how much material you’re using in your design (and to incentivize work-arounds for reloading cartridges)

Experimentation These machines are expensive, with the cheapest ones being the Mojo at around $10,000 USD. If you’re looking to experiment with different materials, I would suggest scouring Craigslist like Have Blue to pick up an older model cheaply.