I knew of 3 shipyards capable of making warships but I was wondering if there were some more…

I didn’t include repair plants, only those yards which make warships.

If anyone else has some other info, if I missed out something important, or if I made mistakes while making this assessment, please correct me:)

There are couple of other shipyards which are building patrol boats, minesweepers and corvette sized ships. All of the mentioned projects are small ships but some of the shipyards mentioned can build light frigates if ordered.

Sredne-Nevsky Shipyard, Leningrad (Project 12700 Alexandrit)

Vympel Shipyard, Rybinsk (Project 12418 Molniya)

Shipbuilding plant Volga, Nizhni Novgorod (project 21820 Dyugon).
Volga is also the shipyard that used to build Ekranoplans and apparently Russian is planning to revive Ekranoplans in the near future.

Yaroslavsky Shipyard (Project 10410 Svetlyak)

Vostochnaya verf shipyard, Vladivostok (Project 10412, Project 21820)

Khabarovsk Shipbuilding Yard (Project 12061E Murena-E)

There are also a couple of other notable shipyards like Vyborg Shipyard which can build vessels with deadweight up to 12 000 tons. Although Vyborg Shipyard hasn’t build anything for the navy since the 80s.

In the future Zvezda-DSME shipyard might be one shipyard that could build aircraft carriers if ordered, although it will be specialized in construction of civil vessels. The new Zvezda-DSME shipyard should be ready in 2012 and it will be interesting to see if Lazarev will be the first ship to get overhauled in the new shipyard. I think Lazarev should be the first one to go in but there are also three sovremennys which one might get overhauled.

This is going to be Russian-Korean joint venture; now it is also in the planning and implementation stages. This yard will be specialized in construction of heavy-tonnage civil vessels and ice-proof tankers. While mobilization, the shipyard is capable to built 1 rank warships including aircraft carriers. It is also planned to establish overhaul/upgrade zone for surface ships and submarines at Zvezda shipyard. The purpose is satisfaction of Pacific Fleet’s (PF) needs in all types of complicated interim overhaul and ship modernization.
http://rusnavy.com/news/navy/index.php?ELEMENT_ID=9183

Following completion, which is scheduled for 2012, the Zvezda shipyard will become Russia’s largest shipyard
http://www.lngworldnews.com/dsme-helping-modernize-russia%E2%80%99s-shipbuilding-industry/