As for me, my favorite Pirate theme is actually not from R2, but from Gex 3: Deep Cover Gecko. Pirate themed level, Cutcheese Island. I absolutely love that track, never get tired of it.
I wouldn’t call it ‘best’ (it’s rather short and, like much of the FFXI OST, very repetitive) but it does suit the ominous setting and tempo of battle very well.
Donkey Kong Country – King K Rool (http://www.youtube.com/watch?v=2O_53rg1o9A)
Skies of Arcadia – Kingdom of Ixa’taki (http://www.youtube.com/watch?v=sOGYxkgClAk)
Final Fantasy V – Pirates Ahoy! (http://www.youtube.com/watch?v=1k4D6oN-gGg)
Suikoden – Island Fortress (http://www.youtube.com/watch?v=pEwVHh3RJFY)
Suikoden – Glorious Island Fortress (http://www.youtube.com/watch?v=i7bHJxCoIJg)
Secret of Evermore – Pirates of Crustacia (http://www.youtube.com/watch?v=rfMCLMT_iCE)
Songs about pirates
Suikoden IV – Oh Sparkling Sea! Oh Sky! (http://www.youtube.com/watch?v=Y583_E4XvT4)
Lost Odyssey – Theme of Pirates (http://www.youtube.com/watch?v=-kqq20ir8wo)
Chrono Cross – Zelbess (http://www.youtube.com/watch?v=Py3mLR0Fa-w)
DuckTales 2 – Bermuda Triangle (http://www.youtube.com/watch?v=c-g1tc8aoN8)
Adventures in the Magic Kingdom – Pirate Stage (http://www.youtube.com/watch?v=xb9C1u–Ge8)
Grandia – Palm Harbor (http://www.youtube.com/watch?v=8vTGr2IzZaY)
The Legend of Zelda: Wind Waker – The Great Sea (http://www.youtube.com/watch?v=mGal2fBQ3EM)
Golden Sun – Set Sail! Through the Karagol Sea (http://www.youtube.com/watch?v=KyIOgjniohA)
Monkey Island – The Crypt ~ Rapp Scallion (http://www.youtube.com/watch?v=rIRT9xw4nuw)
Skies of Arcadia – Air Pirate Secret Base (http://www.youtube.com/watch?v=Yut4clvvqkc)
Suikoden IV – Crossing the Waves (http://www.youtube.com/watch?v=HQkKnxjZj3M)
Super Mario RPG – Sunken Ship (http://www.youtube.com/watch?v=ZXcrEuN2JAs)
Uncharted Waters II – Mast in the Mist (http://www.youtube.com/watch?v=Y_LfQUu7m6o)
K Rool Returns (http://www.youtube.com/watch?v=82gyx1KJl04)
Jib Jig (http://www.youtube.com/watch?v=DSFQxuj2CEU)
Lockjaw’s Saga (http://www.youtube.com/watch?v=wdUNrVzT97s)
Snakey Chantey (http://www.youtube.com/watch?v=qWZDv0CdUB4)
Krook’s March (http://www.youtube.com/watch?v=SW6xqrabrYo)
Kaptain K Rool (http://www.youtube.com/watch?v=Zvg2cKgCLR4)
Granted I’d have to say my favorite pirate related track is Pirate Ocean (http://www.youtube.com/watch?v=mI0drkPjyrM) from Super Monkey Ball: Banana Blitz. Its so chaotic and captures the feeling of an intense naval battle. I might be biased though since Hideki Naganuma composed it and he’s my favorite composer.
Golden Sun – Karagol Sea (http://www.youtube.com/watch?v=KyIOgjniohA)
Skies of Arcadia – Air Pirate Secret Base (http://www.youtube.com/watch?v=Yut4clvvqkc)
May I also add this one here 😉
Tingle’s Rosy Rupeeland – Pirate Ship (http://www.youtube.com/watch?v=9Ey695Y_7Gc)
Obviously, most every track in that game fits the theme of pirates VERY well; especially the opening jig on the title screen.
Merchant Ships From the East – lineage 2
n. sanity beach – crash bandicoot
Also:
Eternal Sonata/Trusty Bell – Seize the Artifact for Tallness
They Made Really Good Pirate Musics. (And It’s Parody of Pirates of Caribbean.) and Shrek The Third Game Has Really Good Pirate Theme Musics Too.
Goddamn is it epic for a game as weird as that one.
just found this. sounds piratey
http://www.youtube.com/watch?v=mQU7ml26JVM
pirateish + best darn end-boss-fight music yet!
edit: has already been suggested (by arthurgolden and lijik) my bad