It's a tough one really pal. I have had both Milltek and Blueflame, the first on an ED30 and the latter on an S3.
The Milltek was a non-res, it sounded well and delivered the desired performance increase as promised in conjunction with the remap. It did get a little droney on the motorway at times and wasn't quite as loud as I would have liked! When it was sold the new owner did have a problem with one of the weld's cracking, however the required part was replaced under warranty by Milltek with no issues. Milltek did have a problem with weld's cracking quite frequently lately due to poor manafacturing, this problem has now been eradicated so i'm told. Would I have one again, probably not as Blueflame are in town
Onto Blueflame, this was a custom TBE with a 100 CEL race cat and some beautifully engineered tips, the exhaust is sat in my garage at the moment and the craftsmanship of it is first class when looking up close. It sounded absolutely mental when pressing on, like no other 2.0 TFSI I have heard to date. It was very well behaved at cruising speeds on the motorway which is a big thing for me, as I do a LOT of motorway miles. A really great system, I would not hesitate to use them again in the future.
I don't know too much about the APR but I am sure other guys will be along to comment.
Hope this helps