Super Robot Wars/D/Secrets

Unlockable	Conditions
VF-11C Thunderbolt or VF-1J Valkyrie	Before the Space route Stage 6 (戦う女市長 エースのミリア！) if Gamlin's kill count is 6 or greater you will get a choice. Choose the first option. If his kill count is 10 or more you get a second choice, choose the first for the VF-1J or the second for the VF-11C. If his kill count is between 6-9 you automatically get the VF-1J. Note: if you get either unit, the stage time limit is reduced from 8 turns to 6.
Glacies (Josh Route)	On Stage 13 (アイスドール グラキエース), convince her with Josh. Then on Stage 25 (生と死の呪縛), choose not to cut the system.
Ventus (Rim Route)	On Stage 13 (運命の風), choose to listen to Ventus' story. Then on Stage 25 (生と死の呪縛), choose not to cut the system.
Gundam Mk-III	Choose to go to Jupiter after Stage 15 (強襲！ギシン星間帝国ベガ艦隊). You will receive this with Roux Louka as its pilot. Note: if you choose the Keilas Guilie route, Roux won't have any unit when she and Judau join after the routes merge.
Nu Gundam HWS	Choose the Keilas Guilie route after Stage 15. Before stage 17 (カイラスギリー攻略戦) Amuro's kill count must be 50 or greater.
BD with Zahme Sau (ザーメ=ザウ)	On stage 18 (背中ごしのセンチメンタル), defeat BD within 3 turns of his appearance.
Marg	On stage 20 (銀河の虎) and stage 27 (誇り高き反逆者), convince Marg with Takeru. On stage 29 of the Helios route (暴かれた真実) convince Marg with Takeru, then defeat him with Takeru. After stage 31 (暗黒の皇帝) choose the Gishin Empire route.
Vayeate and Mercurius	Before Stage 22 (ザール艦隊総司令クロッペンの挑戦！) have Hilde and Noin's combined kill count be between 10-19 for Vayeate and 20 or more for both.
Full Armor ZZ Gundam (フルアーマーZZガンダム)	Before Stage 28 (戦場の父 戦場の子), have the sum of Judau's kill count and Roux's kill count be 40 or greater.
Cannon Cubic, Flame Attack Blazing Cross Slash, and Hyperspace Energy Release	Choose the Helios route after Stage 28 to unlock these hidden moves for Daltanius.
Remove Gaia's Antiproton Bomb	Unlock Daltanius's added weapons by choosing the Helios route. On the Gishin Empire route Stage 34 (死闘！ギシン星最終決戦！) deploy Daltanius, and defeat Zuul with Takeru while Daltanius is alive.
V2 Assault Buster	Choose the Angel Halo route after Stage 28.
Katejina and Chronicle	On the Angel Halo route Stage 29 (幻覚と踊れ), don't defeat either of them (they retreat when you defeat the boss). On the first half of Stage 30 (狂乱のエンジェル・ハイロゥ) fight both of them with Usso. On the second half of Stage 30, have Usso convince Katejina, then Chronicle. After convincing them, defeat them with anyone.
Haman	By the second half of the Angel Halo route Stage 30, Amuro, Kamille, Judau, and Char must have a combined kill count of 400 or more. Kamille, Judau and Char must all deploy and must all survive the stage.
Rose Cosmo Crusher Fifth Pilot or with Zeron	To get Rose as the fifth pilot to Cosmo Crusher, have Takeru simply fight her on Stage 31 (暗黒の皇帝). To get her with Zeron, have Takeru convince her.
Reaction Weapons (反応弾)	Pick the Planet Racus route after stage 31. All Valkyrie units will be armed with these before Stage 33 (決死の防衛). Note: This does not apply to song-using Valkyries.
Gabil	On the Planet Racus route Stage 34 (悪夢の突入作戦) attack Gabil with Gamlin. On stage 35 (響け銀河に オレたちの歌) attack Gabliga with Gamlin.
Sibil	On the Planet Racus Route Stage 35, attack Gelpelnitch with Basara.

Summary of Route-Exclusive Secrets

Male Protagonist (Josh)	Female Protagonist (Rim)
Glacies	Ventus
Earth Route	Space Route
(none)	VF-11C or VF-1J
Jupiter Route	Keilas Guilie Route
Gundam Mk-III	Nu Gundam HWS
Helios Route	Angel Halo Route
Daltanius Weapons Marg (1/2) Remove Gaia's Bomb (1/2)	V2 Assault Buster Katejina and Chronicle Haman
Gishin Empire Route	Planet Racus Route
Marg (2/2) Remove Gaia's Bomb (2/2)	Reaction Weapons Gabil Sibil

Additionally, because the puzzle stages are unlocked one per stage and the total number of stages differs between routes, if you want to play every puzzle stage you must choose the Earth, Keilas Guilie and Planet Racus routes (the Helios and Angel Halo routes have the same number of stages)