My favorite mission would have to be Streets of Bucharest. It's a great mission packed with action, great lenght and you get to drive around killing enemies with a variety of vehicles.

that game when i played it rocked

Played this yesterday. I thought that mission 6, "Night of the Jackal" was the best. I'm not sure if this was by design, but I ended up being really low on ammo, which made for an interesting challenge. It was also the only mission where I found anything with the Q-goggles, but I suspect I may have missed things elsewhere.