First, I put as many cards or tokens as I can fit on the scanner and scan the whole printer bed as a high-quality JPEG image at 600 dpi. If you've got tons of hard drive space, you could probably go higher-res or use a lossless format, but I feel like 600 dpi JPEGs are sufficient. Of course, even 600 dpi is overkill for use in Tabletop Simulator (the main Arkham board by itself is over 200 megs at that DPI), but scanning larger gives you more pixels to play with and makes image clean up easier.

On to cleanup. The first thing you'll probably want to do it run some kind of dust and scratches filter on it, and maybe add some kind of blur to help with the printer dots. I usually use a scanner at my workplace that does both of these things automatically and uncustomizably, so I don't have any real advice on the settings there. After that, I use Photoshop's "Crop and Straighten Photos" to cut the card or tokens into separate files. It's not perfect and sometimes requires adjustment, but it works for most items. Once they are separated, I run Photoshop's "Auto Contrast" on the images, and I then bump up the black levels, because I find that most scanners scan blacks as kind of gray-ish. To do this, I run Photoshop's Levels with a low-end Input of 20 and a Gamma of 1.15.

I have created Actions to automate most of the processes above. After they are done, I sometimes make small tweaks by hand or run other automated processes (for instance, for all the monster tokens, I crop off the scanned borders and then just add a solid color border so everything looks uniform).

Then, all that's left is to save them as the final images. I try to find a decent size that looks good when alt-zoomed, but doesn't make the files huge. There's no real rule here. It depends on the a lot of different factors. My cards and tokens are about 500 pixels wide, but some items may need to be larger and some can be smaller.

I save them as JPEG images. One issue I've seen with other mods is that they are too scared to really crank up the JPEG compression. I think this is a mistake. I save most of my images at 5 or 6 out of 10 in the Photoshop JPEG settings. Does this introduce JPEG artifacts? Absolutely. Are those artifacts visible after the textures have been mapped onto a 3-D model and lit in the Tabletop engine? Not very. By doing this, you can get very small file sizes, which is great for performance. On average, my monster tokens are about 39Kb, but I've seen other people's that are over a meg a piece. I happen to think mine still look very nice.

Two final pieces of advice:
Irfanview[www.irfanview.com] is free, and its lossless "Optimize JPG File" feature, will often get the size of your JPEG's down even further. I used it on every JPEG I added to the mod.

If you are scanning something that has duplicated pieces that are identical (for instance, Arkham Horror has 6 copies of the Wither spell), you only need to make and upload one image. You can then duplicate that card as many times as necessary in Tabletop. Some people scan and upload each individual card, but that requires Tabletop to download and load every single one as a separate texture, so I don't recommend it.