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This adjustable pen stand uses a magnet at the top of the arm to hold the pen upright with only one point of contact at the base of the pedestal. It's adjustable to multiple sizes and styles of pens by raising and lowering the pedestal. The only requirement for it to work is that the pen be able to accommodate a small neodymium magnet. The spalted holly pen in the first photo is a Jr. Zen rollerball which already has a magnet built in to the back of the pen and does not require any modification. The spiral patterned pen is a PSI RAW fountain that has enough room in the cap to glue a small neodymium magnet. See my other Instructable if you're interested in making a pen with a spiral pattern like that.

I designed this pen stand in Fusion 360.

Supplies

Tools:

Laser Cutter
Calipers
Large Binder Clips
2.5mm Hex Key
Funnel
Small File

Supplies:

Wood Glue
Tooth picks and q-tips (optional for spreading glue)
Super Glue or 5 minute epoxy
Button Head Hex Screw M4
Hex Nut M4
1/8" or 3mm thick hardwood. Ocooch and Cherokee are two good suppliers. Please don't use plywood, it will just look ugly.
Laser Mask or Blue Painters' Tape
Rice/gravel/lead weights (to weight the base of the stand)
Scotch Tape
320 grit sandpaper
Paper Towels
B884-N52 Magnet (for the stand arm)
Small Magnet (Necessary for non-magnetic pen kits only, see Step 3)
Boiled Linseed Oil (or another oil of your choosing)

Step 1: Cut the Pieces

Since this design has interlocking pieces, the thickness of the material you use matters. It is intended to be used with 3mm or 1/8 inch wood. As long as the actual thickness, (as measured with calipers), is 2.8-3.6mm, it will work. The files are provided in .ai or .dxf formats.

Measure the thickness of your material with a pair of calipers. Select the next largest file size. For example, if you measure the wood as 3.14 mm, you should use the 3.2 mm file. It's better that pieces fit together loosely than not at all, so always round up, not down.
Download the correct size file in the format you prefer and arrange the pieces as desired.
Apply laser mask or blue tape to each side of your piece of wood and use a credit card to smooth out any wrinkles or bubbles.
Cut out the pieces with your laser cutter.
Remove the pieces from the laser and peel off the masking.

Step 2: Assembly

As you are gluing, use toothpicks, q-tips, and paper towels to apply glue and remove excess. The wood glue will dry quickly, so remove the excess after each assembly step before gluing the next piece.

Find the pieces shown in photo 1.
Apply glue as shown in photo 2.
Roll up the pieces so that the 1st is attached to the 4th as shown in photo 3.
Apply glue to the tabs on the bottom of the assembly and press it into the large square piece as shown in photo 4. Make sure that the pieces are aligned as they are in the photo.
Find the pieces shown in photo 5.
Apply glue as shown in photo 6.
Roll up the pieces as shown in photo 7.
Find the photos shown in photo 8.
Apply glue as shown in photo 9.
Attach the pieces to the assembly as shown in photo 10.
Flip over the assembly and apply glue as shown in photo 11.
Attach the two assemblies as shown in photo 12.
Find the rectangular piece with an oval hole as shown in photo 13.
Apply glue as shown in photo 14.
Attach the piece to the assembly as shown in photo 15.
Find the rectangular piece shown in photo 16.
Apply glue as shown in photo 17.
Attach the piece to the assembly as shown in photo 18.
Find the rectangular piece shown in photo 19.
Apply glue as shown in photo 20.
Attach the piece to the assembly as shown in photo 21.
Find the last large rectangular piece shown in photo 22.
Apply glue as shown in photo 23.
Attach the piece to the assembly as shown in photo 24.
Find the pieces shown in photo 25.
Apply glue as shown in photo 26.
Place the square shaped piece into the notch at the top of the left rectangular piece and roll the pieces together until they all fit together as shown in photo 27. Set this small assembly aside for now.
Find the wooden pieces and the hex nut shown in photo 28.
Apply glue to the piece that has the shorter rectangular notch as shown in photo 29.
Place the piece with the long notch over the short notch piece as shown in photo 30. Make sure that the holes overlap on one side.
Apply glue to the tab on the third piece as shown in photo 31.
Press the third piece into the other two as shown in photo 32.
Drop the hex nut into the the hexagonal hole and glue it in place as shown in photo 33. I used super glue instead of wood glue here because it's better at bonding wood to metal, but wood glue probably would have been good enough. Be careful to avoid getting glue in the threads. Set this piece alongside the small assembly from step 27.
Use a funnel to fill the outer cavity of the main assembly with rice, gravel, lead weights, or anything else that will give it some weight. I don't recommend sand since it might be able to escape from gaps between pieces. Make sure that the rice is flush with the inner boundary, highlighted in red in photo 34.
Find the piece shown in photo 35 and try to fit it over the rice. Note the location of the oval hole in the side of the main assembly and the long notch in the corner of the top piece. The notch should point to the corner that is to the right of the oval hole as shown in photo 35. If there's too much rice to fit, remove some until it fits.
Very carefully apply glue to the areas shown in photo 36. Do not apply any glue to the inner square.
Press the lid on as shown in photo 37. Make sure it is aligned correctly as described in step 35.
Use Scotch tape to tape over the the holes in the lid as shown in photo 38.
Use 320 grit sandpaper on all the surfaces of the assembly, especially the sharp corners, but avoid sanding over the Scotch tape. Try to sand with the direction of the grain to the extent possible. Wipe off the sawdust and remove the Scotch tape after sanding.
Find the round piece shown in photo 40.1 and apply glue to one side. Apply glue to the bottom tabs as well as shown in photo 40.2
Attach the piece as shown in photos 41.1 and 41.2.
Before the glue dries, find the piece shown in photos 42.1 and 42.2. Apply glue to the bottom as shown in the photos.
Attach the piece as shown in photo 43.
Find the last small round piece and apply glue to one side and the bottom as shown in photo 44.
Attach the piece as shown in photo 45.
Find the long piece with the jaggedly notched base as shown in photo 46. The other two long pieces have smoother bases.
Apply glue to the base as shown in photo 47.
Attach the base of the long piece to the top of the assembly as shown in photo 48.
Find one of the two other long pieces as shown in photo 49.
Apply glue to one entire side as shown in photo 50.
Attach the piece to the side of the first long piece on the assembly as shown in photo 51. Do the same for the last long piece in order to attach it to the opposite side of the first long piece. Use binder clips to hold the three pieces together until the glue dries. Make sure that the entire arm is fully pressed into the base.
Find the small rectangular pieces shown in photo 52.
Apply glue to the inside of the notch at the base of the arm that is visible in photo 51. Press the larger of the two small pieces into the glue filled notch as shown in photo 53.
Do the same with the smaller notch at the top of the arm and the remaining small piece. See photos 54.1 and 54.2.
Apply glue to the top and bottom of the B884-N52 magnet and slide it into the notch at the top of the arm as shown in photo 55. If you are only making one pen stand, then it doesn't matter which orientation the magnet is in. If you plan on making more than one though, you need to make sure that the magnets are always oriented in the same way, such as with the North pole facing up.
Find the small pieces shown in photo 56.
Apply glue to one of the pieces as shown in photo 57.
Insert the piece into the top of the arm on one side of the magnet as shown in photo 58.1. The orientation does not matter. Glue the other small piece and place it on the other side of the arm so that the magnet is kept firmly in place. The piece will only fit in one orientation, so if it won't go in, just flip it around so that the longer arm goes in the opposite hole and try again. The stand should now look like photo 58.2.
Find the small piece from step 33. Place the small piece into the center cavity of the base as shown in photos 59.1 and 59.2. The hole on the small piece should be facing the same direction as the oval hole on the side of the base.
Find the small assembly from step 27 and the small square piece that has a circle cut from its center. See photo 60.1. Apply glue to one side of the square piece as shown in photo 60.2 and attach it to the top of the small assembly as shown in photo 60.3
Place the small assembly in the center of the base as shown in photos 61.1 and 61.2. Again, the side with the hole should face in the same direction as the oval hole on the side of the base. If it doesn't fit, use a file to round the corners of the inner square of the base as shown in photo 61.3 and use 320 grit sandpaper to round the corners of the exterior of the small assembly as shown in photo 61.4. Continue to sand and file until the parts slide smoothly past each other.
The stand with adjustable pedestal is now nearly complete. Remove the pedestal and apply an oil finish to all the parts that are accessible. I used boiled linseed oil, but you can use a finish of your choice as long as it isn't thick enough to prevent the pedestal from sliding up and down within the base.
Put the pedestal back into the base with the hole facing the oval hole on the side of the base. Use the hex key to install the M4 screw as shown in photo 63.
The stand is now complete! If you have a Zen Jr., you can adjust the height of the pedestal by loosening the screw, pulling the pedestal up or down, and then retightening the screw. Try to get a height that keeps the pen relatively stable, but still allows an impressive gap between the top of the pen and the bottom of the top of the arm. See photo 64. If you have a pen other than a Zen Jr. that doesn't have a magnet, proceed to the next section.

Step 3: Add a Magnet to a Non-magnetic Pen

You will have to take some initiative with this section because there are hundreds of pen kits and you'll have to test your particular one to see if this will work. I can confirm that it works with this magnet and a PSI RAW kit, and that is what I will depict in the following steps.

Try to find a schematic of your pen kit to help you select a magnet. Check the schematic to see how much space is between the end of the nib and the inner surface of the cap. The magnet you select will have to be thinner than this. Check the schematic again to find the inside diameter of the cap. Your magnet will have to have a smaller diameter than that. If you can't find a schematic, use your calipers to measure the length that the pen protrudes into the cap and subtract that from the inner length of the cap. See photos 1.1 and 1.2 for a demonstration of those measurements. Use the calipers again to measure the inside diameter of the cap as shown in photo 1.3. Try to select a magnet that fits in the allowed space with a case 1 pull force of at least 2 pounds. KJmagnetics.com has a great selection and lists the pull forces for all their magnets.
Use a toothpick or hex key to apply a small amount of glue to the inside of the cap, all the way at the end where the magnet will go. Hold your pen stand upside down and with the cap open end up resting on the bottom surface of the top of the arm as shown in photo 2.1. Drop the magnet into the cap. The magnet in the arm will ensure that it lands with the correct side down on the glue. Pick the cap straight up and away from the magnet in the arm so that the orientation of the small magnet in the cap does not flip. Without changing the orientation of the cap, set it aside far from other magnets until the glue dries. See photo 2.2.