This is my curated list of possible names for ships in Stargate Universe. This list includes only canon nations, meaning nations that were confirmed in canon sources to own a ship. Its a curated list, meaning I removed names for no reason other than I just felt like it. For example, USS Aphrodite is a valid name convention-scheme wise, but poor name for a Warship. This list was extensively proof-read for any Goa'uld names, so altho you could take just list of "Greek mythology figures" and use that, there's a good chance you will be using Goa'uld names 25% of the time, and that's not exactly the message you wanna be sending to the Free Jaffa Nation

United States / USAF

Mythology 

USS Aegaeon
USS Aether
USS Agamemnon
USS Agon
USS Bellerophon
USS Calypso
USS Deiphontes
USS Demeter
USS Diomedes
USS Eirene
USS Enyo
USS Eos
USS Erebos
USS Eurus
USS Geryon
USS Hades
USS Helen
USS Hermes
USS Hestia
USS Hyperion
USS Illiad
USS Lyssa
USS Minotaur
USS Nyx
USS Ophion
USS Pallas
USS Patroclus
USS Penelope
USS Persephone
USS Perses
USS Phoebe
USS Talos
USS Theia
USS Theseus
USS Triton
USS Tyche

People 

USS Carter
USS Emerson
USS Fraiser
USS Langford
USS Pendergast 

Space Program 

USS Antares
USS Challenger
USS Columbia
USS Endeavour
USS Intrepid 

Russian Federation / VVS 

Chelomey
Gagarin
Glushko
Khomyakov
Komarov
Leonov
Mishin
Tereshkova
Tsiolkovsky

 

People's Republic of China / PLA 

Guo Ziyi
Han Xin
Li Guang
Qi Jiguang
Qin Shi Huang
Sun Bin
Wu Qi
Xiang Yu
Yuansu
Yue Fei

 

European Union / --- 

Hastings
Leipzig
Marathon
Marne
Normandy
Orléans
Trafalgar

 

Republic of India / IAF 

INS Ajatasatru
INS Akbar
INS Aurangzeb
INS Samudragupta 

Now, my headcanon is getting a bit too big, to ignore the fact that it may seem that my names are all over the place, I'll try to explain each ship, per each nation, and reasoning behind it. So bear with me, if you want

United States / USAF

USS Prometheus [CANON] - A Titan from Greek mythology.
USS Daedalus [CANON] - A craftsman from Greek mythology.
USS Odyssey [CANON] - A Greek epic poem, but also a Command Module on board the Apollo 13
USS Apollo [CANON] - A god from Greek mythology. But also, you know, the Apollo program. 
USS Hammond [CANON] - Originally named the Phoenix, after a mythical bird from Greek mythology. Now named after George S. Hammond.

Now, this is where the fun begins. We have three angles of attack. A) Being basically anything Greek B) Being Apollo space program and C) Being a very famous Stargate person.

USS Agamemnon [FANON] - A King from Greek mythology.
USS Langford [FANON] - Named after Paul and Catherine Langford.
USS Endeavour [FANON] - Named after Apollo 15 Command Module.
USS Columbia [FANON] - Named after Apollo 11 Command Module.
USS Persephone [FANON] - Named after a god from Greek mythology.

So I think the US naming scheme is obvious. We can say for sure, that they use a mix of A) Anything Greek and B) Famous Stargate people, with potential C) being the Apollo Command Modules. Altho, I think that there are no further suitable names in the C category, as "USS Yankee Clipper", USS "Charlie Brown" or god forbid the "USS Gumdrop" are IMHO awful names.

Russian Federation / VVS

RFS Korolev [CANON] - Named after Sergei Korolev the "Chief Designer" from Cold War Space Race.

So now the next step is, in my opinion, logical, we are looking for the famous Space Race people. Here we plentitude of candidates. Vasily Mishin, Valentin Glushko, Yuri Gagarin or Valentina Tereshkova.

RFS Gagarin [FANON] - Named after Yuri Gagarin, in my opinion, an obvious choice.

People's Republic of China / PLA

Sun Tzu [CANON] - Named after, well, Sun Tzu, a Chinese General, and Strategist.

Now this one seems also logical, we are looking for Chinese General/Strategist/Famous people that had something to do with war. We get names like Wu Qi, Qin Shi Huang, Xiang Yu or Qi Jiguang.

Qin Shi Huang [FANON] - Named after Qin Shi Huang, brilliant strategist and founder of the Chinese Empire, the Qin Empire.

European Union / ---

EUS Austerlitz [CANON] - Named either after unknown city from the Czech Republic, or Battle of Austerlitz.

Now, again, the angle of attack is clear. We are looking either from unknown cities from Czech Republic , or important European Battles. There is no need to actually list examples, as Europe seen a lot of those. I personally went with something more historic, rather than WW1/2.

EUS Orléans [FANON] - Named after Siege of Orléans. Arguably the decisive battle of the Hundred Year War between France and England, that ironically lasted 116 years.

Republic of India / IAF

INS Asoka [CANON] - Named after, I'm not really sure. Most likely Ashoka/Asoka/Ashoka the Great, and Indian Emperor

Now, I  did not give this one much thought, but I presume India would continue with its "Indian Emperor" naming scheme.