Haruka Kanata was so highly regarded that when the dub finally used song for the openings after two seasons of the Narm Charm theme "Rise! Tsuyosa!" (albeit mashed up with third opening's visuals), the whole fandom was BLOWN AWAY.
After almost 10 years, AKFG finally returns to the series to sing Road to Ninja's theme per Kishimoto's personal request. As expected, they didn't disappoint.
The Fifth Season Opener, Seishun Kyosokyoku's melancholy sound and sadly wistful lyrics perfectly captured the feeling of the series at that point, as Team 7 slowly began it final collapse.
The sixth, No Boy, No Cry by STANCE PUNKS. The accompanying animation in which Naruto takes a flying leap off Hokage Rock is especially good in the dub (lacking the original's prominently superimposed "TV Tokyo" logo).
The fourth Shippuden Opening, Joe Inoue's CLOSER, is a beautiful song in and of itself. When combined with Asuma's you should know this by now, but final fight with Hidan catapults it into CMoA status. Also works well as a NaruHina piece.
The band little by little made an opening song for Naruto and a closing song for Naruto Shippuuden that are both made of epic f'ing awesome. Here's the first and the second.
The 15th Opening, "Guren" by DOES and the 29th Ending, "FLAME" by DISH are both mind-blowing, both screaming "Everything just got real!" Prominent NaruHina moment aside, they're notable in that the accompanying animation also both compare and contrast the relationships of love and hate between brothers (between incarnations of Asura and Indra in the opening, and for Obito and Kakashi for the ending.
The 3-on-1 fight between Sarutobi, Orochimaru and the two deceased Hokages sounds more dangerous and exciting and totally kickass thanks to Heavy Violence. And you know the part where Sarutobi is talking to Orochimaru about the Konoha villagers and how the Will of Fire will never fade? Yeah that part.
Toumei Datta Sekai is an awesome Naruto opening. Not only that, but it's also an epic opening sequence. Also slight Tear Jerker, like Sign, due to some of the imagery on the opening. Okay, most, if you know what's going to happen next.
At last, Itachi gets a theme: Many Nights. And they couldn't have picked a more fitting tune.
A place to return to, which just goes to show how much work went into the anime-exclusive arcs in Shippuden.
The first three songs of the 2nd Shippuden OST are simply Hot-Blooded to not be considered awesome, namely: Shouryuu, Rinkai, and Gekiha. The fact that Gekiha has already been used in Naruto's battle with Pain in Sage Mode simply highlights its awesome. In addition, Kokuten sounds somewhat sweet as an anti-Sasuke theme, seeing as they played when Itachi was plucking out Sasuke's eye with Tsukuyomi and when Killer Bee blasted him with a Lariat.
The music that plays in Episode 85 while Shikamaru shocks Kakuzu by summoning a pile of water and then saves Ino and Chouji with Kakashi's help. Listen to it here.
Two Shippuden songs that have only appeared twice each, and neither of them are on either of the currently-released soundtracks, that both deserve to be here. The first is a slow, sad tune played on strings and flute, heard during Naruto's mindscape just before his first 4-Tailed Form transformation, where he's beating himself up over not being stronger, in Episode 41; heard again in Episode 159, when Kakashi dies and laments his failure to protect his teammates, as spectres of his old team disappear in front of him. The second song, which turns Ominous Pipe Organ up to 11, has been heard twice: once in Episode 41, when Naruto started to transform into 4-Tailed Form, his flesh tearing away and forming a cocoon of black chakra around him; and again (this time accompanied by ominous chanting) at the tail end of Episode 166, when Pain stabs Hinata and gives his little "Love breeds sacrifice, which in turn leads to hatred" speech, and Naruto proceeds to go 6-Tails.
In Episode 167 of Shippuden, there is Hisou, possibly the most epic soundtrack in the entire series. It plays again the second time Naruto is shown defeating Deva Pain and when Danzo flashes back to Sarutobi being named Hokage and attempts to kill Madara.
Nakushita Kotoba ("Lost Words") by No Regret Life, the ending theme of the original anime's last non-filler arc. Beautiful and terribly sad, appropriate considering Naruto and Sakura's reactions to Sasuke's departure.
THIS. When you hear this, expect badassness in the form of Gaara.
Shutsujin, or Departure to the Front. An awesome song fit for a hero's glorious departure—or return, as it were. One notable occasion this is played is at the end of Shippuden Episode 175: Naruto's triumphant return from defeating Pain.
There are two noteworthy unofficially released soundtrack pieces. One is the theme that plays during Jiraiya's death, and the other plays after Chouji wins his fight with Jirobo.
There's an awesome track that first plays in Shippuden Episode 329, when Naruto first pulls off the Tailed Beast Transformation and proceeds to throw down with the Tobi-controlled 3- through 7-Tailed Beasts.
The theme which plays for the final five minutes of Episode 329. The combination of tragedy and optimism is incredible. Every moment of action it plays behind is immediately made more powerful just by its mere presence!