I'm busying working my way through the boxset right now and I have some thoughts
Iron Man - a great introduction to exciting near future of the cinematic Marvel Universe. Funny and action packed, it's not often that origin movies are so much fun.
Iron Man 2 - expands the universe, the first real introduction of the sort of epic against all odds battles that comic book movie adaptations often neglect to include. I watched this second as it is a direct sequel to Iron Man so the two are much easier to watch back to back. It also goes a good way toward letting the audience know about SHIELD without giving the game away regarding their whole operation.
The Incredible Hulk - I made the mistake of watching this third instead of second. Probably the darkest film of the series watching it between the two Iron Mans felt like it would jar but I've learnt otherwise. It takes us right into the murky underworld of military conspiracy which sets the Marvel Universe apart from the ridiculous supermen of the DC one. It also acknowledges the cultural currency of the character by dropping us straight into the action with minimal origin fannying about.
Thor - It's very rare that comic book movies are able to show off the scale of the universes that the comic mythology have established over the decades. By this point in the series familiarity with the Marvel canon is becoming essential to get what's going on. If I had watched Iron Man 2 in it's rightful place the escalation in scale beyond the hero vs villain rivalries of normal superhero films makes this a great establishing piece that sets up the wider universe and further expands on the work of SHIELD.
Captain America - a bit of a pause in the series we get the most everyman of the Avengers, and coupled with Thor, this serves primarily as a prologue for the full cast Avengers film. Whilst being arguably the most enjoyable of the individual hero films it is also probably the one which stands alone least best.
Avengers/Avengers Assemble - an absolutely terrific job of tying together the various plot strands from across the previous five films. As well as drawing together character who seem so comfortable alongside each other despite their own films not being entirely similar in tone. Every comic book fan might wish to see their favourite heroes team up in an onscreen world which actually looks like the one they've been reading all these years but I bet no one thought that you'd actually be able to get the look of a superhero epic on screen so successfully.
I am a little worried that in the run into Avengers 2, with Iron Man 3, Thor 2 and Captain America: Winter Soldier, we will see the series start to suffer under the bloated weight of continuity which occasionally stifles ongoing comic book series and makes them so uninviting to those without hours to spare on Wikipedia.