Short ETFs hold derivatives, such as options, futures, and swaps, to attempt to track the inverse (or sometimes a multiplier of the inverse) of an index, on a daily basis (so not 'over time' but each day mirror the performance of that index).
SH, for example, holds the majority of its exposure in S&P500 Index swaps with various banks:
http://www.proshares.com/funds/sh_daily_holdings.html
30% in a UBS swap, 17% with BofA, 15% with Goldman Sachs; about 85% of their exposure is in these swaps. They then hold enough cash to cover all of these positions (they're officially listed as having a 200% position in cash and a -100% position in various deravitives).