The Beast Wars music is very different from the music of the old show. 
The music in every show is largely or wholly performed for that individual 
episode -- I actually heard this from Bob Forward himself.  Robert Buckley 
is the show's sole music composer (he also does Reboot and 
War Planets, IIRC), working from a bank of synthesizers.

 Some of it has the "cheesey action music" feel of the third season pieces,
with lots of generic electric guitar; other parts of it sound like World
Music, with flutes and "tribal" sounding instruments.  Overall it is not
as strongly melodic, but it sometimes is more mature-sounding than much of
the original series' music.  Another big difference is that there are 
significant periods in the show with no music at all. 

About a dozen or so different themes recur regularly and comprise the 
bulk of the background music; many of these are frequently repeated or 
even played over one another, two or three at a time.  There are also little 
snippets (like Silverbolt's horn fanfare) that pop up frequently.  I wouldn't 
be surprised if some of the music is recycled, but I'm not willing to watch 
the episodes enough times to really find out for sure.  :)  Anyway, the 
point of this list is to catalogue all the themes as thoroughly as possible. 


THEMES:

Beast Wars Theme:  Obviously, the theme from the show's opening. 
Variations of it are used to soundtrack much of the show, especially the
battle sequences.  For reference purposes, I'll break it up into several
sequential parts: 

 * Gathering Pace -- the dramatic opening synth chords (as the ships are
falling out of the sky) and the progression of ascending guitar notes that
follow them, up to the first climax.  Heard in one or two of the first
season shows that start off with shots of the orbiting stasis pods.

 * Pursuit -- steady paced action music, with some jaunty percussion
followed by the electric guitar playing the same three-chord progression
several times.  Starts after the ships have crashed in the first-season
opening, and contains the first two shoutings of "Beast Wars!" in the
second-season version.  Heard in "The Agenda" III, when the Maximals
attack the Ark. 

 * Battle -- In the second season version of the BW Theme, this part
starts after the second shouting of "Beast Wars!" and goes to the end.
Trilling guitar, then several punchy synth chords which build in
intensity, up to the end of the opening theme.  Similar trilling guitar is
often used to soundtrack aerial fight scenes.  That same trilling guitar
is heard in "The Probe" as Optimus flies past Rattrap and Cheetor in the
show's beginning.

Desperate Measures: Intense battle theme, a jauntier version of the
Pursuit section of the Beast Wars theme.  Heard in Coming of the Fuzors II
as Megatron and Inferno fire on Rattrap and Dinobot from the air; Before
the Storm as Tigatron flees the Predacon base; and -- I think -- Code of
Hero as Dinobot takes out Inferno and Blackarachnia.

Land of Mystery: sounds like an electronic flute, if there is such a
thing.  Often heard as the camera closes in on one of the bases,
especially at the beginning of episodes.  Almost a snippet; only four
notes define the melody.  "Feral Scream" Part 1 as Depth Charge heads out to 
hunt Rampage; "Feral Scream" Part 2's opening pan across Cheetor's quarters.  
Commonly segueways into....

Wild Lands: Jaunty little four-note progression that often accompanies the
Maximals on their journeys.  Heard in "The Web" as Rattrap goes hunting
for Cheetor.

Haunted Lands: Long, low synth note, that steps up for a moment, then steps 
back down.  Used to set an ominous mood at the beginning of several episodes -- 
most notably "Go With the Flow"'s opening sequence.

Serengeti: A subdued but fast-moving action piece, with
tribal-sounding flutes overlying a very percussionistic rhythm: the type
of music they'd play over a wildlife documentary about Africa.  Heard in
part one of the pilot episode, when Cheetor is running alongside the other
cheetahs; "Other Victories" when Cheetor is chasing the merged 
Tigatron/Airazor spark.  Similar to the above piece.

Aftermath: Tense, high-pitch single synth chord.  Opening of "Aftermath" (Rattrap
sitting at the computer); "Nemesis" Part 1 as  Silverbolt and DC search for the Preds. 

Celestial Destruction: Grandiose piece driven by a smashing guitar chord
followed by two  long synth chords underlain by a vocal chorus.  Heard
whenever something big and disastrous is happening.  Accompanies the
scenes of planetary ruin in Other Voices II; the spreading time wave at
the end of Agenda III; the incoming quantum surge at the beginning of
Aftermath; the beginning scene of Before the Storm when Tigatron sees the
alien device.

Mongo Celestial Destruction: same as above, but all guitar instead of
synth/vocals.  Heard in "Bad Spark" as Megatron "welcomes" Rampage to the
Preds; in "The Agenda" part one's opening, as we watch the transwarp wave
expand outwards; "Nemesis" Part 2's opening as Megatron blows up the jungle.

Tigatron's Theme: gentle flute music, solemn, almost mournful.  One of the
show's best mood pieces.  Heard several times in "The Trigger" as the
camera pans across the flying island's landscape; .

Cosmic Significance: choir-driven piece heard in "Chain of Command"
whenever something happens involving the alien site.  Sort of a fusion of
Celestial Destruction and Tigatron's Theme, and rather derivative of the
Ark theme from the movie "Raiders of the Lost Ark".  Beginning of "Spider's
Game" when we see the orbiting pods; beginning of "Nemesis" Part 1 when 
Tigerhawk is making lots of sparklies and Optimus reads from the Covenant of Primus.

Dark Place: another slow flute piece.  Not as sad as Tigatron's Theme, not
as sharp as Land of Mystery; somewhat dark.  Heard in Other Visits as
Tigatron and Airazor close in on the alien site; in "Code of Hero" as we
close in on the early humans' valley in the beginning; in "Bad Spark" as
BA and Silverbolt start their journey to the mountain top.

Predacon Theme: four note progression heard in a variety of styles:

* Forceful version: "Dark Designs" when Rhinox is stomping down the
corridors of the Pred base; during Airazor's first few seconds of
existance in "The Spark".

* Delicate version:  in "Double Jeopardy" when Blackarachnia first comes
on screen (I think!)

* Creepy version:  done with off-key or dissonant chords.  Often used 
when the spiders are shown.  "Code of Hero" as Tarantulus closes in on 
the animal caught in his web; at some point or other as the spiders are infiltrating 
the Axalon in "Other Voices" part 1.

Silverbolt's Theme:  anyone who's seen "The Agenda" doesn't need this one
explained to them.  The piece is one of the few light-hearted bits of
music in the show and provides some welcome relief from all the grim
seriousness.  Heard several times in "The Agenda" as we follow Silverbolt
flying through the air, for example when he's on his way to meet
Blackarachnia in part 1.  It's the fully developed version of his fanfare,
which is four or five notes of muffled trumpets (or some other horns) that
accompany Mr. Nobility any time he gives one of his little speeches in the
earlier episodes.  Easily the most villified piece of music ever to grace
a Transformer cartoon. 

Sad Endings: Dark, mournful piece done with low synthesizer notes, that
shows up whenever the Maximals have lost a fight or some such.  Heard at
the end of "The Probe"; "Feral Scream" Part 1 when Depth Charge reports
Cheetor's "death"; "Nemesis" Part 1 when the Maximals are in Tarantulas's 
submarine chamber.  Similar to...

Theme of Hero: Dark, quiet synth notes, almost as if backed by male
chorus.  Heard in "Bad Spark" at the end of Dinobot's one scene; "Code of
Hero" when we see Dinobot alone in his chamber.

Flight of the Waspinator: frantic trilling synth piece derived from the
classical piece "Flight of the Bumblebee".  Heard in "A Better Mousetrap"
when Waspinator is buzzing around mumbling to himself; in "Maximal No
More" when Waspinator shoots down Silverbolt; a variant play in "Nemesis" Part 1 
as Waspy, QS, & Inferno fly off to look for a new colony.

A Little Tension: four synth notes that usually rise in pitch with each successive 
playing.  Similar to the second part of the "Gathering Pace" part of the BW Theme.  
"Feral Scream" Part 2 when Optimus interrogates Depth Charge.

Black Death: male chorus backing some kind of synthesizers, but blended so
you can't really  make out either one clearly.  Almost a sound effect,
rather than a music piece, but it's purely there for mood -- it adds a
sense of horror.  Heard in "Dark Voyage" when the snake is crushing
Cheetor; in "Bad Spark" as Silverbolt starts to cross the log, and again
just before BA and Silverbolt run into Rampage; "Feral Scream" Part 1
right before Dinobot 2 captures Depth Charge; "Nemesis" Part 1 as Megs and DB2 
approach the Nemesis.

BITS 'N' PIECES:

Dawn of Man: No, not Also Sprak Zarathrustra; it's the acending 
synth/choral blend heard at the end of "Code of Hero" as we zoom away from the 
protohuman and his newly-discovered tool; "Nemesis" Part 2 as Optimus is on the shuttle remembering those who fell during the Beast Wars.

Ultimate Crisis: Repeated series of synth notes.  Heard in "Chain of 
Command" as the alien probe zaps Optimus; "Crossing the Rubicon" when 
Silverbolt dive-bombs the retreating Tarantulas.

Nice Catch: Happy little series of synth notes, sometimes with an angelic 
chorus, that signifies the good guys pulling off some victory.  Based on 
Silverbolt's Theme, I'm given to understand.  "Bad Spark"
when Silverbolt catches BA at the very end; "Go With the Flow" when 
Rattrap catches Oona in the Pred installation; "Changing of the Guard" when 
Silverbolt catches Rattrap (right before they collide with Depth Charge); 
"The Agenda" Part 2, when SB catches BA (again!).

Maximal Victory: A punchy, upbeat, anthemic series of ascending synth notes, 
signifying some triumph for the good guys.  "The Agenda" Part 1 when 
Megatron is arrested by Ravage; "Master Blaster" as Megatron is 
driven out of the volcano by the Maximals; "Nemesis" Part 1 when Optimus 
mistakes Rampage's detonation for the destruction of Nemesis.

Oooo Ahhh:  The "awe-inspiring" electric guitar chord heard every time a
character arrives or transforms impressively or for the first time.  Watch
the series premier to hear it about twenty times in various incarnations.

Meanwhile Back at Base: quick ascending series of xylophone notes, often
used when cutting from an action sequence to a non-action shot in the
Maximal base.

Bad News: two pairs of ascending horn or synth notes, usually heard at the
end of a scene -- in particular the sort of scene that ends with Optimus
saying "That's just prime."  "Code of Hero", end of the scene where Rhinox
announces the transwarp wave will alert Cybertron to their location.

Uh Oh: off-key decending synthesizer note, the sort of thing heard in
horror movies when the killer is lurking nearby.  Heard in "The Trigger"
whenever one of the traps is activated; at various points during "Bad
Spark"; once or twice as the submersible launches in "Nemesis" Part 1.

Draw, Partner!: Strumming of a guitar and a single harmonica wail, heard 
whenever a Western theme creeps into things (ie the end of "Coming of the Fuzors" 
Part 1, CotF Part 2, and "Maximal No More" when Quickstrike and Rattrap have it out.)
Reapears in "Feral Scream" Part 1 when QS goes after the TM2 Cheetor.

DAT's Gotta Hurt: quick descending tuba notes, often heard when someone
falls or splats Warner Brothers-style.  See "The Low Road" (like when
Waspinator bounces away at the very end) and "Before the Storm".