OK, I discovered the source of problem! HID broke some games since r236 (r235 works good). When I turned off HID option and connected GameCube controller problematic titles are running fine. So..., here is updated version of my previous compatibility list (r251, Wii, usb, shrinked isos, ocarina off, hid off, vmc on [59 blocks], progressive off, widescreen off):
1080 Avalanche - works without any problems. With HID on stucks on title screen pretty often.
Baten Kaitos - works without any problems (music plays fine!),
Baten Kaitos Origins - works without any problems (music plays fine!),
Bomberman Generation - works without any problems. With HID on stucks on loading screen (it's broken since r236. R235 works without any problems),
Eternal Darkness - works without any problems. With HID on stucks on poem screen [Edgar Allan Poe: "Deep into..."] (it's broken since r236. R235 works without any problems),
F-Zero AX - works without any problems (save card isn't emulated yet),
Legends of Wrestling - stucks on loading screen (after movie intro),
Luigi's Mansion - works without any problems, but you can't watch "Pikmin Movie" (included in the options),
Mario Kart Arcade GP - works without any problems (save card isn't emulated yet),
Mario Kart Arcade GP 2 - works without any problems (save card isn't emulated yet),
Metal Gear Solid: Twin Snakes - works with one minor exception: controller doesn't work/respond on first screen (when you can choose to play with progressive on/off). I noticed that this is earlier problem (long before r251),
StarFox Adventures - works without any problems. With HID on stucks during first Fox McCloud mission (when you ends fly through rings - it's about 4% of game),
Virtua Striker 4 ver. 2006 - console turn off after/during boot,
Wave Race: Blue Storm - works without any problems. With HID on stuck on title screen (it's broken since r236),
XGRA Extreme G Racing Association - works without any problems. With HID on stucks during loading the race pretty often.
1080 Avalanche - works without any problems. With HID on stucks on title screen pretty often.
Baten Kaitos - works without any problems (music plays fine!),
Baten Kaitos Origins - works without any problems (music plays fine!),
Bomberman Generation - works without any problems. With HID on stucks on loading screen (it's broken since r236. R235 works without any problems),
Eternal Darkness - works without any problems. With HID on stucks on poem screen [Edgar Allan Poe: "Deep into..."] (it's broken since r236. R235 works without any problems),
F-Zero AX - works without any problems (save card isn't emulated yet),
Legends of Wrestling - stucks on loading screen (after movie intro),
Luigi's Mansion - works without any problems, but you can't watch "Pikmin Movie" (included in the options),
Mario Kart Arcade GP - works without any problems (save card isn't emulated yet),
Mario Kart Arcade GP 2 - works without any problems (save card isn't emulated yet),
Metal Gear Solid: Twin Snakes - works with one minor exception: controller doesn't work/respond on first screen (when you can choose to play with progressive on/off). I noticed that this is earlier problem (long before r251),
StarFox Adventures - works without any problems. With HID on stucks during first Fox McCloud mission (when you ends fly through rings - it's about 4% of game),
Virtua Striker 4 ver. 2006 - console turn off after/during boot,
Wave Race: Blue Storm - works without any problems. With HID on stuck on title screen (it's broken since r236),
XGRA Extreme G Racing Association - works without any problems. With HID on stucks during loading the race pretty often.