Abandonware is flourishing. It's technically pirating, but in most cases the games are so old, or the rights are owned by defunct companies, that nobody cares. Yet, it's easy to see how the scope of abandonware has broadened in recent years. Even relatively recent games, or games available on "Collection" packs from publishers, are popping up on abandonware sites. Once the finances of the publisher are in question, it's quite likely to strike back at abandonware with the same force it attacks normal pirates.
The solution? Prevent abandonware. Release your old, defunct games for free. Whatever company now owns the rights to Pirates! Gold, do you really think you're going to sell it again? Is it going to devalue your share price if it's released on your website?
Keep inventories for sale through the website. People have been clamoring for copies of FreeSpace 2 for years now, driving the prices through the roof on eBay, and Interplay has only now, after four years, decided to re-release the game. I'm sure that in three years they'll notice a similar situation is developing with Sacrifice.
Publishers - use old games as promotions for new products, as Gathering has done with Hidden & Dangerous, by releasing the game for free to coincide with the shipment of H&D2 to stores. Put license limitations on so that only you can host the game on your website to drive traffic to the online sales section - just do something. Don't sit on a property, it's not getting you any value that way and it's still being downloaded online.
I also don't understand this paranoia over releasing source code. id Software does it and with great success. The releases have breathed much life into Doom, Quake and Quake II, and the free games made with those engines help promote id by stating where they got the technology. Microsoft has earned thousands of fans by releasing the source code for Allegiance recently, a game which they no longer planned to sell or support. Gamers are blindly loyal, it's one of their endearing qualities and terrible traits at the same time. Look at the three-way rivalry between Total Annihilation, C&C and WarCraft, or Unreal vs. Quake vs. Duke.
Granted, it's a bad idea to release code in some circumstances - like if you plan on re-using network code in a future game or if the game is still being popular online - but it keeps interest on the game. No community project is going to be as good as a sequel.
There are a few games just begging to be released free or re-released. A free Tribes, for example, would make a great marketing promotion for Tribes: Vengeance. Since so few people were willing to take a risk by buying Tribes in order to play it, they never saw what a great game it was. Well, release it now and you get a free advertisement for T:V - "More! Better! Faster! Better Looking! Buy now!" Battlezone, another game that didn't get a chance, is a license begging for another take on it. Offering the game up for download could get people excited for a future version. I can't even find the game on the official Activison website, for crying out loud.