When I play Nautilus, I pick him whenever my team is lacking magic damage, then focus on building a lot of flat magic pen while remaining really tanky, so the enemy is forced to build MR or allow me to do crazy amounts of damage for a tank, especially if they try to ignore me. If you're looking more for CC spam, a build focused on CDR would be more appropriate, but I feel that other tanks, like Alistar, fill that role better.
Runes: magic pen marks/quints, flat armor seals, flat CDR glyphs with 1 MR/level
(Note: these might benefit from some tweaking to be specific to Naut, as I use these pages for other champs, as well)
Usual start: 2xDoran's Shield, Boots, Health Pots (grab a Null-Magic Mantle and 1 Doran's if you see a lot of magic damage on the enemy team)
My usual build (in whatever order is most appropriate, usually focusing on tankiness initially): Sunfire Cape, Abyssal Scepter, Haunting Guise, Aegis of the Legion