You can silicone acrylic to glass, but it's not a terrific connection. It's totally inappropriate for a pressure application (ie. an acrylic base and glass sides on a tank) but holds up perfectly well for zero pressure/impact settings like a sump baffle. As Rusty said, check the type of silicone you buy. You want either Silicone I or Silicone II - do a little reading to find out which, I've forgotten. One is safe for aquarium use and the other can be rather toxic.
For glass, just look up glass in the yellow pages. Typically you'll find a few and even autoglass places sometimes cut and sell plate glass and just don't advertise it because it's not a significant enough part of their business. They might carry acrylic as well. I've heard of a few folk getting scrap acrylic from bigger glass/plastics suppliers, but that can be hit and miss.
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