so much out there to use. we've gone with a 45 mil EPDM and trench it in like atook says for some of our small fire ponds. We would use a HDPE boot with stainless steel straps for penetrations (dry hydrants). We haven't partially lined any ponds as i assume you're thinking about so i wouldn't know about anything to look out for in pond bottom trench anchoring, but i'd bet there is a red flag to catch down there. we cover the liner w/ soil for protection and I've heard that it's hard to walk or stand on a 3:1 sloped wet/underwater liner.
cheers,