Here are two lists of all the themes that got remixed in the
official albums and
fighting games.
In addition, U2 remixed all of ZUN's original themes for the fighters (Demystify Feast, Night Falls (this is the SWR remix), Missing Power, Legendary Fish, Catastrophe in Bhava-agra, Unknown X and Lost Emotion).
Bloom Nobly, Ink-black Cherry Blossom ~ Border of Life, Voyage 1969, Catastrophe of Bhava-agra ~ Wonderful Heaven and Unknown X ~ Unfound Adventure all have last spell themes modeled after them. Then there's Theme of Eastern Story (as mentioned), which occurs in a lot of title themes (including the pre-title screen theme for LLS and MS), Retribution for the Eternal Night ~ Imperishable Night, History of the Moon ~ Gensokyo Millenium, A Midnight Fairy Dance, Led by a Cow to Visit Zenkou Temple, Bamboo Forest of the Full Moon, and Illusionary Joururi (and prolly a few other things I'm forgetting) and the IaMP main theme which is all over the fighters (notably Broken Moon).
Then Ran and Yukari's stage and boss themes from PCB are inspired by each other (can't really say which one came first) and there's a Speed Fox(!) remix for Charming Domination; Cirno, Lyrica, Youmu (stage), Mystia and Reisen have their themes remixed in PoFV (and BAiJR for Cirno) and Wind God Girl was featured in StB (though it seems to be unaltered). There's probably a few other things I missed (especially the ending and credit themes), but that should be enough for now. Feel free to correct me if I got anything wrong.