Just about any drawing tool (pen, pencil, marker, engraver...) that is not too big or heavy, can be attached to the pen-arm and used for plotting on eggs and spheres. In choosing a pen, a number of questions come into play:
- Precision - How thin a line do you want? How much detail is needed, vs. bold lines?
- Permanence - "Forever" or erasable?
- Surface - What are you plotting on? Eggs, glass, ping-pong balls, etc. all have very different surface textures and ink absorption.
- Expense - Are you doing ultra-fine, archiveable work or rapid-fire demo's? Pen price and longevity vary tremendously.
 Pen size
The basic Eggbot pen-arm comes with a 3/8" (9.5 mm) diameter hole. Without requiring custom modification, a pen must fit in this hole, whose size was chosen to mate with ultra-fine point Sharpie brand pens. You can also get different distal pen arms, with a larger hole sized to fit wider "fine point" Sharpie markers, as well as blank ones, where you can drill your own hole.
To use a much wider pen that will absolutely not fit in the hole, you can also use this hack with a binder clip.
 Popular Pen Choices
Commercially available permanent "Sharpie-compatible" markers that fit into the standard pen holder:
- Sharpie Ultra Fine point Ubiquitous and inexpensive (~$1), this is a great pen to start with. It comes in a wide variety of colors, is permanent, and has a relatively fine tip. The larger "Fine Point" size Sharpie markers will not fit in the standard pen holder, but do fit in the "wide" pen holder. (The pen holder on the EggBot Pro does fit both Fine and Ultra Fine point Sharpie markers.)
- Sharpie Micro Same as above, but half as long. More expensive (~$1.40), not as much ink per pen (and fewer color choices), but the smaller pen will not bounce around as much as its bigger brother. (You may need to order these online.)
- Tul ultra-fine point Similar to Sharpie in quality, tip size, color availability and price. [As of 16 aug 2016 no longer available at officemax/officedepot]
- Copic Multiliner SP series Significantly more expensive (~$8), but offers a choice of much finer tips (nibs), plus both the nibs and the ink cartridges are replaceable. These are harder to find, though you may find them at local art supply stores like Dick Blick. They can be ordered online from Blick, Amazon, and others. There is also a cheaper, disposable ("non-SP") Multiliner series that is not Sharpie-compatible in terms of size, but will fit in the pen holder of the Egg-Bot 2.0 kit.
- Pigma Micron series Like the Copic Multiliner SP, this is a nice, technical fiber tip pen, and offers a variety of nib sizes, though not as tiny as Copic. It is Sharpie-compatible, but not as "nicely" as the Copic. It mates to the pen-arm higher up on the pen, and requires more force. Easier to find than Copic, it is disposable and ~$3.
- Martha Stewart Crafts .1mm Writing Pen These markers come in only a few colors. The marker body is pretty close to the Ultra-Fine Sharpies, so they work well for detail work in conjunction with those. These markers are very light and need a little extra weight to make them work right – it helps to put the cap on the butt of the marker. $8 for 4 pens. [As of 16 aug 2016 the pens are no longer available. A broader (1.2 mm) tip set of 36 Martha Stewart markers is at amazon]
- Rapidograph by Koh-I-Noor. Recommended to purchase a cleaning kit with the pen and clean it after use.
- Staedtler Pigment Liner. Indelible, waterproof and lightfast.
- Staedtler Mars Professional. I have used Staedtler for years for technical and pen&ink drawings and they are my favorites. Staedtler makes the Mars Matic line as well with points down to .1 mm which is as good as it gets (AFAIK). There is a 4 pen set, comprising of a 0.25,0.3,0.5,and .07. It is a very nice set though relatively expensive ($24 approx). Comes with a closable plastic case, and the pens are excellent. If you are happy with the Sharpie Ultra-fine, then this would be a good step up. Works well on Ping Pong balls, wood spheres and glass. May come off on glossy plastic, but that turns out to be a good thing when you are experimenting.
- Pilot Gold/Silver Markers. They are the type that you have to occasionally have to shake. If you break the design up into many layers you can use these pens, it is just a matter of making sure you don't move the pen arm when taking the pen out and shaking it and putting it back in. The smaller the amount you have to fill in the better the results. The extra fine point is between a fine point and medium in the sharpie. They dry relatively fast as well, not quite as fast the Identipen, but pretty close. Available at Amazon.
- Uni-Ball Signo Broad Point Gel Impact Pen White Ink. These are ball-point, and have a claimed 1.0 mm tip. They work surprisingly well at least on eggs, so perhaps on other textured surfaces. They need to be primed just immediately before use, a fingertip is even better than a piece of paper. Once they get going they work pretty well, putting down a viscous, opaque, not-too-wide, not-very-many-skips line. They are far from instant drying. Available at amazon.
 Food safe markers and pens
- AmeriColor Gourmet Writer Food Color Markers by Ateco. Felt tip marker with a long slender conical tip. Fits in standard pen holder. $17 for set of 10 markers on Amazon. Also available in 2-packs of black.
- Wilton FoodWriter Fine Tip Edible Color Markers a.k.a. Foodoodler Food Coloring Markers by PLP Inc. Felt tip marker with a short fat conical tip. Can fit in the standard pen holder at the closest point to the nib. Indexes nicely into the "wide" pen holder. $8.50 for five markers. Often available in "seasonal" color pairs at grocery stores in the US.
- Kopykake Edible Ink Pens. Double ended marker with fine and bold tips. Bold tip end is tapered and can be slid to various heights in the standard pen holder, which may make registration between color changes difficult. Fine tip end is stepped rather than tapered, and is a little narrower than is ideal for the standard pen holder, but would index at the same height from one color to the next. $10 for ten markers.
 Less-than-ideal markers and pens
- 120 Markers on first look appears quite desirable. The set has a myriad of color choices, and is extremely inexpensive. However, the colors have been found to diffuse into egg shells over a period of hours, softening or smearing the inked lines. The diffusion appears to be color selective, such that initially-black lines may even end up appearing blue. The inks are water-based, and take rather a longish time to dry. They could nonetheless be useful as fill colors, since diffusion from the edges may be masked by an outline. Here is an image comparing 120 Markers and Sharpie ultra fine markers on eggs.
- Uni-ball Signo Angelic UM-120AC Gel Ink Pen 0.7mm might look worth a try, but in fact they skip terribly on eggs (though they are terrific on paper).
 Other writing implements
- Gel and rollerball pens. These types of pens do not work on all surfaces, but the ink does flow quickly, which may be beneficial for fast plotting. A review of seven different pens is posted on jenslab.com.
- Pencils. Must be sharpened and will wear down during the plot, possibly varying line width.
- Mechanical pencils. Attention must be paid to the tip as it wears down throughout the plot.
- Chalk (e.g. on egg painted with chalkboard surface). Must be sharpened, and wears down quickly.
- Mechanical erasers (e.g. on graphite covered egg).
- Brush pens. The Platinum Souhitsu Fude Brush Pen CFS-250 apparently works well in the Eggbot.
 Alternative tool heads
Many things that are not traditionally writing implements can potentially be used as well. For example,
- A simple needle, for drag-etching a soft surface
- Kistkas, for traditional pysanky. Evil Mad Scientist now produces an Electro-Kistka for the Eggbot.
- A mechanically vibrated diamond point, for engraving hard surfaces like glass. (An official diamond point accessory is offered by Evil Mad Scientist).
- An air-operated (lightweight) high-speed engraving tool for engraving many materials.
Barrels: Not all pens are Sharpie-compatible (in terms of barrel size). Non-Sharpie compatible pens are indicated above along with any required pen arm modifications.
Pigments: Not all pens are permanent. Type of ink should be indicated above.
Nibs: Manufacturers' stated nib sizes are far from straightforward to understand. Terms like "ultra-fine" are subjective. But numerical specs should be regarded with some skepticism as well. Micron's size descriptors are not in mm ("005" = .2mm). And Copic's smallest nib is ".03mm" -- a quick check with a calculator reveals this is ~1/1000 of an inch. Which is finer than a human hair. It's tiny, but not anywhere near that small! Of course, these numbers refer to the width of lines the pen can make, not the nib width. This value depends greatly on pen pressure, surface texture, and feedrate (speed of drawing).
Extremely fine color plots: Replacement ink cartridges for Copic's Multiliner SP series come in two types (A and B). These are related to different pigment carrier formulation for different nib sizes (A for the smallest, B for larger). Unfortunately, they do not make "type A" color cartridges (the smallest nib is .3mm for color). However, tests mating color cartridges with .03mm nibs show good results with some, but not all colors. The "A" formulation inks require longer drying times: handle your eggs carefully when using the "A" formulation so as to prevent smudging.
Variable pen heights between Sharpie-compatibles: Different brands of pen will be held by the pen-arm at differing heights above the egg. Doing multicolor plots with tight color registration is far easier with all pens being the same brand.