As good as HL2 is - possibly one of my favourite games ever - it most certainly isn't the most well made game. There were loads of teething troubles, getting Steam to work, endless patches and updates to get it running smoothly... And the infamous stutter bug.
ID seem to make well made games. Been playing Doom 3 since I bought a new GFX card last week - runs great and smoothly, looks fantastic, no bugs, no crashes... They do good netcode as well.
Grand Prix Legends should get a mention (well, it would from me) purely because at the time in 1998, being able to race an online field of 20 racers was amazing. The GPL netcode was amazing, very stable, and well written.
Deus Ex was a well written game too, good story, no stability problems, ran well and looked good even on modest hardware at the time... One of my all time favourites in fact.