Well, with Black Mesa just having been released, I'll have to say that's my favourite Source mod. It's amazing, it really is. It's basically HL1 remade with the Source engine, though expanded and lots of small details in it, in case you haven't heard about it.
Another mod I'd to mention is Minerva: Metastasis. It's set on a small island with a high Combine concentration and you're sent to investigate why. It's got the high level design quality of Valve, but instead of horizontal it's vertical, meaning you'll go down instead, which is a cool, different approach of doing it. It's so good in fact, that the guy behind the mod was hired by Valve, after he finished it.
Dear Esther is also worth checking out, as mentioned by DazZ.
Other mods I haven't played yet, but heard good things about are Mission Improbable and 1187, though that'll be remedied soon(ish), but I've heard good things about both.