Came to say Prodeus but Ion Fury is worth a look. Not sure if that counts as Indie though. Project Warlock is fun too. Devil Daggers is more like arena based. Lots out there.
I was going to uhm akschully your post, but I learned that 3D Realms is the publisher while Voidpoint is the actual developer. Not sure where Ion Fury lies in that case...
Speaking of 3D Realms-published boomer shooter throwback games,
CULTIC is pretty good, at least that's my impression from the demo. If you liked Blood, you'll probably like CULTIC too.