It always has to be Nemesis for me, in my opinion it's as close to perfection as Alton Towers has ever come with a new ride. The layout is amazing, the pacing of the various elements, the speed through the heavily banked helix and just the way it interacts with it's landscape. That is what I think lifts Nemesis up above all of the other coasters at Alton Towers.
I would say that second place would go to Oblivion, it's simple but hugely effective. I remember being absolutely terrified by it the first time I stood underneath that drop. The various theming elements and videos across the whole area all work together to deliver something quite impressive, I don't think this all works as well though these days with The Smiler being directly opposite. Personally, X Sector just doesn't feel as intimidating as it did say 5 years ago, I think this is partially down to The Smiler but also maybe just part of growing up too.
I really like Th13teen, I think it's a solid ride that is quite well themed, just the marketing let it down hugely. We new all along that it wasn't going to be an all out thrill machine. I don't know why they tried to market it this way, it led to a lot of negativity that could of easily been avoided.
The Smiler, is a great roller coaster, it's intense and it does what it was intended to do very well. The theming is well done, even if there is too much grey concrete and the various effects aren't always working. I just don't find it all that fun to ride repeatedly, not in the same way as the others.
Air is also a great ride, but I feel it was let down by an incongruous choice of theming and a layout that is really far too short and lacks anything really forceful. Obviously it was an expensive and complex prototype and there were limits to what could be done with it, but I just think they could of done a little bit more.
The other three I don't think are in the same league as the above. They are all fun rides, however with the exception of RMT they lack the thought and attention to detail that have gone into the other coasters. That's not to say they aren't welcome additions to the park, they are most definitely, and as you can see from typical queue times they are very popular with the general public. I just don't think you can group them with the Secret Weapon type rides.
Anyway, that's enough rambling from me.