Nectar and The Night And the Silent Water have some similar acoustic stuff, it might be intentional though.
The first riff in The Leper Affinity is an updated version of Powerslave by Iron Maiden.
The beginning of the guitar solo in Serenity Painted Death reminds me of Pull Me Under by Dream Theater.
The Drapery Falls and I Transpire by Katatonia have much in common. Don't know which of those songs was made earlier.
That has probably been mentioned but the rap parts in Ghost of Perdition and The Grudge by Tool are very similar.
The grand majestetic riff in Black Rose Immortal around 4 mins reminds me of that big Gary Moore hit, was it Over the Hills And Far Away?