Very tough question to answer but I'll try...
1) UYA will always be one of my favorite games period and #1 in the series for me.
2) ACIT really polished off a lot of things and it looks the best by far.
3) Going Commando was great.
4) TOD was good but it was definitely not the best.
5) One thing I'll give Deadlocked is that it had a great weapon system.
6) Ratchet & Clank gives off a lot of nostalgia and was a great place to start.
7) Size Matters was pretty lackluster, at least once it got ported to PS2.
I haven't played QFB or Secret Agent Clank.