If a student needs just a little extra help, I write fingerings above the music - no colors. This is not that different from what I do to remind myself of tricky passages!
If a student needs a little more support, I write in the fingerings (in pencil or pen) and use highlighters to denote which string the notes should be played on.
Orange = C or E string
Blue = G String
Green = D String
Pink = A String
Yellow = dynamics, pizz/arco, or other relevant information
If students need less visual clutter (for whatever reason), I have made sheets that look like this one. The rhythmic representation is a little tricky (I try to use spacing, but it is not precise), but usually these kids will figure out the rhythm by ear.
Finally, if students do not have the coordination to use their left hand fingers, I have open-string versions so they can play along with us. I like to avoid this if possible, because then they aren't hearing the melody of the song coming out of their instrument, but I have had a couple of instances where this seems to be the best option. This can be combined with a little bit of colored tape (think washi tape) on the edge of the fingerboard beneath each string to make it clear which one is which.
Over the past five years, I have used this system with about 40 students, with great results! This doesn't always mean that they learn to play really well or that they necessarily continue playing, but I have gotten positive feedback from the students, their families, and the special education professionals at my school. In the end, it helps the students be included, accepted, and able to play along with us without the barrier of reading.
I feel a constant tension of pushing students to be able to read music (and up the tiers) while still providing them with the tools to have a positive experience in orchestra. I don't pretend that I get it right all of the time, but I do know that I have some students in 8th grade now who would never have found the joy in making music if they hadn't gotten a little help with reading music in the beginning! To me, that is worth it.
As always, I am happy to share the materials I have made - feel free to send me a Tweet (@ms_a_yeh) or leave a comment if you are interested!