I've been seeing a lot of people say that their mods were deleted when TF2 updated to use Steampipe. That isn't what happened at all.
The mods are still there, they were just moved to the download folder.
In order to use them again, you need to either dig them out of the download folder or re-download them from where ever you got them in the first place. Go to the Team Fortress 2 folder, open the tf folder, make a new folder named custom. In custom, make another folder and name it whatever you want to. I called mine mods. From there, set the mods up just like they were before the Steampipe update.
For example, I have a custom sound for the Shred Alert taunt. In order to use it, I put in in Steam>steamapps>common>Team Fortress 2>tf>custom>mods>sound>player
The taunt's sound file is in the player folder. In most of the mods from Gamebanana.com, you just need to put the folder that is one step beyond the tf folder in your mods folder.
If you have any questions or mods you want to share, post 'em here.