I just became aware of Protoculous, a compressed version of Prototype and Script.aculo.us.  It works the same as the uncompressed version, but reduces the size of both from 215k to 131k.  Using gzip compression seems to bring it down to around 32k.  It’s currently in my development branch and I plan on using it with the next major update for Property Center.  If you’re using Prototype but not Script.aculo.us, I’d suggest having a look at Protoculous anyway.  He includes a compressed version of just Prototype that reduces the size from 96k to 59k.  Gzip compression continues to reduce that to around 16k.