I mark my ball with a red line under the number and then a black line under that red line.  Easy to spot from a distance and does not look like any other marked ball out there.  Very obvious!   Note:  I once played with a guy who said he does not mark his ball because it changes the flight of the ball!  What???

Even tho it's custom, I still mark the green " T " to the right of the number.  If someone spells their last name the same, they are related to me, and their are a lot of relatives who play the local course.  Currently, I think there is 8 of us who are current members of the local course with the same last name.  The 29 is my wife's birthday, it's not so I don't forget, but more so that I always think of her while playing, her encouragement to play, play well, and have fun keep me going back. 

I started marking my Pro V1's with a black dot above & below the Titleist logo.

a #7 with three dots.  One at the top, two on the bottom.

I put a green line that I use to line up my puts. The line is under "Titleist." 

On my custom Titleists, I use the same markings as on my other Titleists, a green dot above and left of the "T" and a blue dot below and right of the final "t".  Here are my custom balls--shouldn't really need to mark them:

These are last year's.  This year's are the same.  70 is my age.  They'll be good for another 6 months, then I'll have to order a new number.

I always start my round just before tee off with a blue line across the pro V 1x  and 1 blue circle to the left of the number. Never been questioned about which ball is mine.. 

Douglas

I fill a dimple with a black dot under the number on both sides of the ball. 

I mark my ProV1X with a blue dot down and to the left of the number!

I mark mine with a smiley face under the number

I mark my Titleist with a drawn match stick man in red.

Always one blue dot just left of the titleist logo

University of Virginia V's in a snow storm pattern.

Mine usually get a green square around the number 

I mark with my grand kids initials. SC on one side, MC on the other. My fellow members are always returning my lost balls they have found.

Greg Tachiera

Round Hill CC 

Alamo, CA

I always draw a line under the ball name... between the name and the ##s

jln