Okay, I'll re-explain what I said in the shoutbox here so it doesn't disappear as quickly.
You do not need to create your own pak files for anything, as pak files are obsolete with the death of WON. Go get Steam as it will update your version of HL.
Sounds need to go into your modsound folder. This is valvesounds for use in HL, cstrikesounds for Cstrike, nspsounds for NS, and so on .
To play the sound file, use an ambient_generic. To make someone say the sound, like a Scientist, use a scripted_sentence. You'll need to add a sentence name and the file path to the sentences.txt to make it work in the latter situation. I believe we have tutorials on doing that.