"Running Fire" with honorable mention to the DS version, which loses some complexity but changes the flavor for the better.
There's also the absolutely beautiful "Flower of Happiness", played during the best ending's credits. Presented in-game as an instrumental, but also a lyrical version from the soundtrack.
"Lord Laharl's Hymn", the original vocal hub theme, which sounds fittingly grand and awesome for Laharl; it was good enough to return in almost all subsequent games in an almost as awesome 8-bit version for the Item World mystery rooms since.
Although it's exclusive to the game's North American translation due to copyright issues, "Invasion from Within" by Tsunami Bomb is an excellent rock song that gets you pumped for the fights it plays in.
Hour of Darkness also gives us "Disgaea", the epic Final Boss theme that couldn't fit the battle against Seraph Lamington more. It was good enough to be reused in Disgaea 2 for some of the fights against Laharl, ironically enough.
Returning from La Pucelle Tactics is "Great Wilder", a kickass Arabian-sounding theme that accompanied Baal's Optional Boss appearance in one way or another ever since. Also check out the original version from La Pucelle, the remix from Makai Kingdom and the version from Disgaea 4 onwards, which are equally as awesome.
"Visual Sensation", which plays in the battles for the chapter leading up to the final boss. Very fitting, especially given that those battles are happening inside a mansion, and the tune has a very elegant feel to it.
"Last World" and "DEAD END" are also extremely awesome. (If you listen closely, you'll notice that "DEAD END" is actually a more dramatic version of Wanderer's Poem.)
"Blue Concerto", especially the arrange version, which manages to be both epic and beautiful.
"Nether Institute Evil Academy" and "A Song For You". "Nether Institute Evil Academy" is well-known for the dance number in it's opening, but the song itself is rather infectious and is reminiscent of "This is Halloween", especially toward the end. "A Song For You" differs from most of the Nippon Ichi ending themes by being rather upbeat and Broadway-ish, but that's what makes it one of the most memorable themes.
"Makai Fugue". Best evil sounding song in the Disgaea series.
The "Maritsu Evil Academy Entrance Applicant Recruiting CM Song", also known as the game over theme. Never has there been a more chipper and bouncy song about the fact that you just got your ass handed to you. The song is very likely making fun of you for losing, given the game it's from.
Great Glider, an awesome Arabian-inspired track that's reminiscent of "Great Wilder". It was good enough to be reused in Disgaea 5 as the Item God theme and for a couple of post-game battles.
Finally, Asagi gets her own spot in the limelight! The damn inspiring "Asagi, GO Fight!!", which plays at the end of Asagi Wars during the final boss battle and her Heroic Sacrifice, and returned in Disgaea 5 untouched.
Fuka takes the stage. "You Go Girl" kicks in. You know you're in for a good time.
"The Fuka and Desco Show" brings another excellent vocal theme: Sadistic Emotion.
"Hold You Back", a worthy successor to the first game's Disgaea and the second game's Disgaea Rhapsody.
"Piano Sonata D No. 4", essentially the successor to the previous game's "Blue Concerto" and it plays during the second phase of the fight against Fuka's killer.
"Crimson Cross", an excellent song for Valvatorez's fight against the Netherworld President and for the first phase of the fight where Fuka gets serve out justice against her killer.
Nisa'stheme from the second game. The most hot-blooded theme Tenpei Sato has ever created. And that N! I! S! is extremely catchy.
"Moving Express", the boss theme for several characters. The piano portions of the song are especially beautiful.
"Dramatic Devil Story", which makes the final battle feel especially epic, combining the guitar, drums, violin, piano, and haunting vocals Tenpei Sato is known for in most of his best works into one haunting, chaotic, and epic symphony.
Lieze Love, wonderful and calming song that plays during most of Liezerota's scenes. This song also has a couple of notable variations. One is called Lieze Lullaby, the game's beautiful ending theme. The second is the rather kickass LieZe Rock, a Dark Reprise accompanying the final boss battle against the Void Dark possessed Liezerota.
Bitter Sweets, a haunting tune that plays during the boss fights with Majorita, featuring a sinister choir and some badass guitars.
While Moving On is slower and more tranquil than past hub themes, it's no less excellent, sounding very beautiful despite the Gratuitous English.
Kill Real continues the series tradition of having awesome opening themes, and is also awesomely used in the final battles against Bloodis and Void Dark. It even comes complete with a few German lyrics!
Whether you fight the senators who refused to pass your bill or watch Killia unleash his Superpowered Evil Side, Stepping Hard Beat is there to get you pumped up.
On the tear-jerking front, Silent Sadness is a beautiful track that does a great job of accompanying sad moments, even serving as effective Sad Battle Music against Usalia's zombified parents.