Hey Polly! I am new to this site, thus the reason for what seems like a late response to your question/concern. There is a wonderful book called "1001 Great Ideas for Teaching and Raising Children with Autism Spectrum Disorders" by Ellen Notbohm and Veronica Zysk. In their book they address everything from social skills to clipping toenails!
Some of the suggestions posted by others are actually used in their book for clipping toenails along with others:
Always clip after bath or shower when nails are soft.
If doing all ten fingers or toes at once is intolerable, do one a day in constant rotation as part of the general bedtime routine. Work up to two per day, etc.
Encourage the child to do it her/himself as early as possible.
Stabilze the finger over the edge of a hard surface such as a counter, table, book, or knee.
Have Dad or a sibling trim their nails at the same time. They can take turns.
Recite a favorite rhyme, poem or story and personalize it by using his/her name.
Try it while they are totally engrossed in the favorite TV show/movie.
The fine-paper side of an emery board may be more tolerable and has the added benefit of eliminating sharp snags. Keep up with it on an every-few-days basis.
When all else fails, do it while they are asleep. (Which I noticed you said you already do but maybe you'll have to continue with this until your child is a little older and able to tolerate it better. The last thing you want to do is cause your child to fear toenail clipping anymore than they already do.)
Search the internet for adaptive devices. Comfort Care Baby Nail Clippers by The First Years come with an attached magnifying glass (decreasing the chance of nipping tender skin) and large grippers for better control. LilNipper Clippers are plastic-encased clippers with a slot in the faceplate that the child slides his/her finger into, never actually seeing the clipping mechanism. Munchkin Saftey Nail Clipper has a plastic safety guard and a safety-grip ring underneath to slip your finger through, steadying the clipper.
Anywho, these are straight from the book I mentioned! It's a great book to own.
God bless you!