Like recycling, some little things together make a big positive impact. What's an expression for "a little thing that adds to the common good"?
Forgive me for stepping off topic; but as an old non-profit hack I suggest you stop and think whether that's really what you want to say.
If you happen to know that your donor is a P.G.Wodehouse fan, you may remind him of Wodehouse's fondness for “Every little bit you get added to the little bit you've got makes just a little bit more”; but I would be wary of appearing to rebuke him for having given only “a little bit”.
I suggest a better approach would be something like this (of course I’m making up the numbers; you must be very careful to be accurate):
Thank you for your generous gift of $17.25.
We are now 5.8% of the way toward our goal of $1,000,000. That leaves us quite a way to go, of course; but your donation at this early stage helps critically towards building momentum for this initiative.
If you happen to think of others whom we might approach for support, with whom your name would carry some weight, I would very much appreciate your dropping me a line at the email address above.
Gratefully yours, &c
With any luck your correspondent will jump at the opportunity to demonstrate his connectedness, and provide help that doesn't cost him anything out of pocket. He may enjoy the opportunity to have you hold up his acquaintances and rivals; and he might even increase his donation and give you permission to mention the amount, in the hopes that a base spirit of emulation will increase the bite on them.
I've seen, in certain contexts, "a teaspoon" used. It's in the sense of the expression about "emptying the ocean with a teaspoon, but acknowledging that if that's what's needed then we'd better get working with our teaspoons.
I see it quite a bit amongst the "social justice" community (feminists in particular, but also the related bits of the gay rights, anti-racism and trans* communities).
I think the origin is this (2007) blog post: http://www.shakesville.com/2007/12/me-and-my-teaspoon.html
It's certainly not in wide-spread usage, but it fits the sentiment you want.
How about something based around The whole is greater than the sum of its parts?
So the individual donations add up to a certain amount of money, but together they create opportunites and community spirit.
Or maybe his donation has given impetus or set the ball rolling.
The spark that starts the fire.
From little acorns come mighty oaks.
What about contribution ?
Besides referring to a gift or donation, it also means
contribution: something given in common with others for a common purpose; a portion, share or part.
If you want to be literal at the risk of sounding petty, you can express your thanks for the "small contribution".
If you want to be gracious, you can express your thanks for the "thoughtful contribution" without referring to its size at all. You might also say "helpful contribution".
Personally, I would not bring too much attention to the size of someone's gift while I am thanking them for it. But it should not stop you from letting them know that you recognize that it was both helpful and thoughtful. It would not even be wrong to describe it as generous, even though you consider it small yourself.