Whenever you download and install a game on Steam, the files rest neatly on your hard drive like a well-pressed stack of laundry for quick access and organization of custom mod files. Some older Source games creak along on an older format from an earlier age in Steam's saga, but in a new FAQ, Valve says it's converting the guts of these games to use the SteamPipe content delivery system for faster load times and an updated file layout.
Counter-Strike: Source, Day of Defeat: Source, Half-Life 2: Deathmatch, and Team Fortress 2 will soon traverse over to the steamapps/common section of your Steam folder instead of the older steamapps/ destination. The conversion is automatic: Valve says you'll need enough disk space "for about two full copies of the game" as it changes over.
Modders and mod users have a little bit of extra homework to do to ensure everything works. Custom files will need to be copied manually over to the new directory, and mod authors should start packaging their works as VPK files instead of in a ZIP.
ZIP files still work in a pinch, as Valve describes it:
"For example, if the ZIP contains custom player models that look like (heaven forbid) ponies, and one of the files is materials/models/player/scout/scout_head.vtf, then you might make a dirctory such as tf/addons/i_love_ponies. You should unzip the mod such that the custom scout head texture ends up at tf/addons/i_love_ponies/materials/models/player/scout/scout_head.vtf."
Check out the rest of Valve's FAQ for more detailed info on the changes SteamPipe brings. You can also download and join the ongoing Team Fortress 2 beta to see the updates for yourself.