Below are just some of the types of mods that a pinball owner might make to their machine.
Cliffy protectorsA practical mod that protects vulnerable exposed edges of playfield that are prone to wear. Cliffy protectors are something that I think is almost a given for pinball owners, and should be for pinball operators as well. It not only protects the value of your machine, it helps ensure that your machine will be in good condition 10 years from now. You can read more in my interview with the creator of Cliffy's Pinball Protectors.
ToysSmall action figures can literally be affixed to the playfield. Our Lord of the Rings has tons of them, and we just added some to our new Avengers machine. My favorite mod of this type, however, is the mini arcade machine we put in TRON that is actually emulating the original TRON arcade game code. So awesome. So meta. There's also the Merlin mod you can add to Medieval Madness: holding a lit color-changing crystal ball. Check out this thread about modding the Vokswagen van in JunkYard.
LED LightsOne of the first things we do with most of our new acquisitions is replace the older incandescent lights with LED lights. These tend to be brighter, but burn much cooler, which is better for nearby plastic parts (anyone who has seen the damage incandescent bulbs can do to the clock in Twilight Zone knows this all too well). There are all sorts of options for varying the intensity and color of LED bulbs. Cointaker is a good source for conversion kits, but most experienced pinball collectors purchase individual bulbs vs. kits, for a more customized end result.
There are different camps of opinion on LEDs, but the good news is, you (or the next owner of your machine) can easily swap back to incandescent if you prefer.
Under-cabinet LightingI don't see this mod around very often, but we added it to TRON: Legacy when we were first getting into modding. You can buy LED strips that go underneath the machine, and you can wire them in to specific triggers, like flashers, to make the under-cabinet lighting also flash in time with a specific event. Pretty cool.
Color DMDThe only full-color DMD I've seen so far is in Medieval Madness, but WOW, what a difference it makes. You can't get color DMDs for many games yet, as they take a lot of coding to create. I believe the next one being worked on is Star Trek: The Next Generation, and I think Addams Family is also available.
Powder coatingPowder coating is a very dramatic way to make a given pinball machine stand out as unique. I have never heard of a powder coating job that made a machine look bad (unless it was a bad powder coating of course). It does involve prying the siderails off your pin, and the coin door as well if you want to be thorough.
Custom blue powder coated trim on Medieval Madness (Avengers Hulk LE comes with green trim)
Shakers and Audio UpgradesShaker motors can be added to a machine to cause it to reverberate during certain moments (for example, when multiball is about to kick off in AC/DC). This is a cool mod to do, but one side effect you can run into is that it causes the playfield glass to rattle. Enter another mod; anti-rattle tape for the edges of the glass.
Re-themed machinesSometimes people go WAY beyond the relatively tame modifications mentioned above and completely re-theme a machine. This involves not only changing the look of the playfield, but also re-coding the programming. It's the ultimate mod, but certainly one that will make your machine uber-unique. Two examples I know of this are one where a guy pulled off a Ghostbusters theme, and quite recently, a 1975 Abra Ca Dabra machine was re-themed into "Evil Mansion, a hand-painted LSD-themed pinball machine." Now that's creativity.
I'm sure there are loads of other mods to mention, but those are some that we've encountered so far.