Xenogears vs. Neon Genesis Evangelion
Proving that Xenogears is the vg equal (or rip-off) of Eva
First we will look at the simularities between characters.
 
Fei Fong Wong Shinji Ikari
1. Has major identity crisis 1. Has major identity crisis
2 .Destines pilot of Weltall 2. Destined pilot of Eva-01
3. Tries to prevent evolution of humanity 3. Tries to prevent evolution of humanity
4. Unfriendly terms with father 4. Unfriendly terms with father
5. Special connection to Weltall (Slayer of God) 5. Special connection to Eva-01 (Shinji's mother)
6. Has innate piloting ability 6. Has innate piloting ability
7. Mother is dead 7. Mother is dead
8. Unwilling to pilot at first 8. Unwilling to pilot at first
 
Elly VanHouten Rei Ayanami
1. Love interes of Fei 1. Love interest of Shinji
2. Part of Solaris conspiracy 2. Part of NERV conspiracy
3. Turns out to be caretaker of humanity (Miang) 3. Turns out to be mother of humanity (Lilith)
4. 2nd embodiment of Miang after Fei's mother 4. 2nd embodiment of Shinji's mother
5. Absorbed into Dues as part of final plan 5. Absorbed into Lilith as part of final plan
6. Betrays Deus's plan 6. Betray's Gendo's plan
 
Citan Kaji
1. The helpful informant 2. The helpful informant
2. Double agent for Solaris 2. Double agent for Seele
3. Triple agent for self 3. Triple agent for self
4. Has nice garden 4. Has nice garden
 
Wiseman/Grahf Gendo Ikari
1. Turns out to be Fei's father 1. Is Shinji's father
2. Turns out to be enemy 2. Turns out to be enemy of NERV
3. Part of Solaris conspiracy 4. Part of NERV conspiracy
5. Redeems himself in the end 5. Redeems himself in the end
 
Weltall Eva-01
1. Mind of it own 1. Mind of its own (literally)
2. Goes beserk 2. Goes beserk
3. Connects directly to brain (omnigear) 3. Connects directly to brain
4. "True Weltall" is hostile 4. "True Eva" is hostile
5. Part of Solaris conspiracy 5. Part of NERV conspiracy
6. Composed of strange parts (black boxes) 6. Composed of strange parts (organic and angel)
Misc.
Here are things that both the story of Eva and the story of Xenogears share.
  1. Both have large religious undertones
  2. Jewish mystecism (Path of Sephiroth)
  3. Both about human evolution
  4. Humans turn out to be same as enemy
  5. Humans turn out to be one being ( Wave existence = 3rd impact)
  6. Totally different story and objectives in the end than from the ones in the beginning
  7. Story takes a drastic turn from fighting/fun based to tragic/philosopphical based about halfway through (2nd disc for Xeno, and about ep.16 for Eva.)  
  8. Crash of a crucial, alien lifeform in a southern, ice-capped area.
  9. Existence of massive, angel-like enemies who cannot be touched due to a special type of barrier that only the gears/mechas can break.
Other placed Xenogears "borrowed" its story from
Soylent Green
You must be inept ot miss this one

Grandia
1. Outside of Dr.Alma's office in Grandia, there's a sign that says the EXACT same thing as the sign outside of Dr.Citan Uzuki's house in Xenogears-"Bring your sick, injured, etc., but don't bring them dead!"
2. In both Grandia and Xenogears, you play a paper-rock-scissors minigame with a townsperson.
3. In both Grandia and Xenogears, there's the case of an attractive, blond-haired male general who is worshipped by a small group of his female officers. In Grandia, this is Col. Mullen and his 3 underlings, Nana, Saki, and Mio. In Xeno, this is Ramsus and his female Element underlings.
4. Perhaps the most visible thing is the presence of a sprite/character graphic that is pretty much exactly the same. Notice that the sprite for one of the races in Zil Padon, I believe it's the horse-head-like Alquada, is the exact same sprite used in the city of Dazil (or perhaps Aveh) for one of the strange dwellers there.
If I have missed something, gotten something wrong, or put something up you disagree with, feel free to contact me at dirac@cyberspace.org

Much thanks to nm9 for additional info, and the Grandia info.