Digging this up from the grave a "bit". Was looking for remixes of this series myself and this was one of the top hits on google, figured I'd add to the thread with what I found, so that others who find this thread via google or otherwise have that much more.
These two albums stood out to me in my search;
MegaMusicMix - http://colis.jp/?page_id=388
My first trance mission!![ROCKMAN EXE2/Opening Theme]
Your Only Destiny[ROCKMAN EXE 2/You Can't Go Back]
WWW跡地 – ROCK Arr.[ROCKMAN EXE Transmission/WWW跡地の電脳世界]
Black * White[ROCKMAN EXE 3/Opening Theme]
Mega Xross MiXX - http://colis.jp/?page_id=708
VS. Gospel / ROCKMAN EXE2 Arrange:5*LEAF
FINAL TRANSMISSION / ROCKMAN EXE3 Arrange:suimyu
VS. PROTO / ROCKMAN EXE3 Arrange:狛犬
Battle With Myself / ROCKMAN EXE4 Arrange:negi
Hometown / ROCKMAN EXE5 Arrange:3R2
Liberate Mission / ROCKMAN EXE5 Arrange:ice
The Black * White track can be heard in full on soundcloud and is crazy good, probably my favorite of all of these tracks. I actually love that it starts out kind of almost...generic in a sense, the memorable tune plays once softly, and then just BAM, the song just goes full ham. Love it, really feel like it did the tune justice.
Not sure where these albums could be bought from in full, but they are out there somewhere. They hit some of the major tracks I like at least, missing MMBN3 Sad Theme and MMBN2 Kotobuki, but the arranges, especially from the first album, really make up for that I think. Awesome stuff.
edit: Also of course, since the last activity in this thread, the OCR MM 25th Anniversary Album came out, which has a drop-dead amazing arrangement of the hometown theme on it, can't go without mentioning that!