Valuations for startups that received angel or venture funding fell by 25 percent, from a median of $3.9 million in the third quarter of 2008 to $3 million in the fourth, according to new data from Angelsoft.net.

The New York company provides software for angels and VCs to manage their deal flow, and it says this is the largest drop in the four years that Angelsoft has been gathering these numbers.

It’s risky to generalize about the broader funding environment from this data, but Angelsoft tracked a significant number of deals — 123 in Q3, and 128 in Q4. (That’s out of 2,000 startups that apply for funding through Angelsoft each month.) The company says 450 angel groups and venture funds use its software.

The trend isn’t surprising, of course. Back in October, VentureBeat Editor Matt Marshall said the downturn would lead startups and VCs to intensify the battle over valuations, with the VCs holding the advantage; other industry observers made similar predictions. Angelsoft says the average pre-money valuation listed on funding applications actually held steady from quarter to quarter, implying that investors bargained them down.

In the announcement, chief operating officer Ryan Janssen says it was “damn near a miracle” that Angelsoft processed more deals in Q4 than Q3. Now, that probably says more about Angelsoft than it does about venture investing – I certainly don’t believe the total number of venture deals increased in Q4 – but given the concerns about a decline in early-stage investments, that’s still an encouraging sign.