I am pretty much obsessed with video game music, let me get that out of the way first.
Second off, for those who can manage to navigate a Japanese website, a large group of people from 2ch run polls for favorite video game music (the recent one, the 6th annual ranking ends on Saturday actually, and here's a link to the videos for the
5th) and put together a wiki
over here, and I've personally been following it since the OP/ED rankings done at the beginning of this year. Definitely worth a look if you're really into this kind of stuff, you find a lot of new songs that you never would have found out about elsewhere.
Anyway, as for my favorite songs I'll just copy/paste my vote for the recent poll (descending order, of course):
http://www.youtube.com/watch?v=w-r0DIoQ_iA Pursuit ~Cross-Examination - Gyakuten Saiban 2 (Phoenix Wright: JFA)
http://www.youtube.com/watch?v=Szr0TSXcWok Fly to the Leaden Sky - Battle Garegga
http://www.youtube.com/watch?v=EjuOuIkythI Pursuit - Hokkaido Rensa Satsujin: Okhotsk ni Kiyu
http://www.youtube.com/watch?v=TAy3nlATLkk Gensokyo Millennium ~History of the Moon - Touhou Eiyashou ~Imperishable Night.
http://www.youtube.com/watch?v=v5FR_i-EbDc Danger - Secret of Mana
http://www.youtube.com/watch?v=ggGPqnkCihY 02 - Kirby 64
http://www.youtube.com/watch?v=lBaoMKoABlY Last Battle -T260G- - SaGa Frontier
http://www.youtube.com/watch?v=PfST-dLgGcQ The Flame and the Arrow - Rudra no Hihou
http://www.youtube.com/watch?v=lsSm6CgCF6M Clocktower's Beat - Haunted Castle
http://www.youtube.com/watch?v=cL_xLGoLcx8 battle on the plane of holy - Dragonseeds (so good it's being recommended twice in this thread :D)
http://www.youtube.com/watch?v=PDZYS7Gc5TQ Decisive Battle - Final Fantasy V
http://www.youtube.com/watch?v=sF--oI9R8zw Boss Battle - Battle & Get! Pokemon Typing DS (when music in an educational game is better than that of the actual series...)
http://www.youtube.com/watch?v=OnA51R7NzHQ Confidence in the domination - Valkyrie Profile
http://www.youtube.com/watch?v=7_a8zstttak [Senritsu] SHUDDER - Einhänder
http://www.youtube.com/watch?v=Hl22NRJ00GY System - Sin and Punishment: Star Successor
http://www.youtube.com/watch?v=G6hd8NOqVpI Running Hell - Cave Story 3D
http://www.youtube.com/watch?v=gVy030vTigc FAKE - Darius Gaiden
http://www.youtube.com/watch?v=DIxCemuJYDc Rainbow Road - Mario Kart: Double Dash!!
http://www.youtube.com/watch?v=_pcobhFVGLM Explorer ~Closed Town - Megami Tensei II (skip to 12:05)
http://www.youtube.com/watch?v=EqCcrIxNVBE DON'T LEAVE ME ALONE - Nemesis 2
http://www.youtube.com/watch?v=DkEG5KrldSo BOSS 6 - Night Striker (only first part is from the game, also see
here)
http://www.youtube.com/watch?v=25m3Gk7mRQM Pushing onwards - VVVVVV
http://www.youtube.com/watch?v=OvqLnwRqo6g I'LL SAVE YOU ALL MY JUSTICE - The Scheme (Did I mention Yuzo Koshiro is a god? Well, he is.)
http://www.youtube.com/watch?v=dwtASYeer8Y MEGALOMANIA - Live A Live (Too bad Yoko Shimomura is an even bigger goddess)
http://www.youtube.com/watch?v=h-9kyLrXglY WE'RE THE ROBOTS - Mega Man 9
A few others:
http://www.youtube.com/watch?v=QWsWAuJRJuk ChoroQ City "PARTY ROOM" - ChoroQ3
http://www.youtube.com/watch?v=wu5IBULcPPw Ending - Vampire Killer
http://www.youtube.com/watch?v=nZ6ABV_Q9qU Megalith -Agnus Dei- - Ace Combat 04: Shattered Skies
http://www.youtube.com/watch?v=K6gdyiLZxJ8 ZERO - Ace Combat Zero: The Belkan War
http://www.youtube.com/watch?v=B5GCwnaEmVo SILVER LINING - Eschatos (By the godly Yousuke Yasui)
http://www.youtube.com/watch?v=XqsNkD-FPEs YO-KAI Disco - Mamoru-kun wa Norowarete Shimatta! (more from the god Yasui)
http://www.youtube.com/watch?v=DT5Gsk7tSzE Counter Strike - NEW Eijukugo Target 1900DS (Yousuke Yasui's most obscure work, probably. Did I mention it's Yasui? It's Yasui.)
I literally could go on forever about my favorite tracks, but I fear I've gone overboard already ^^; Hope you guys find something new you like, whether it be here or elsewhere!