Inventory Slot Detection

As of 14w10c, this is possible using scoreboard values.

First, you need to set up a dummy scoreboard variable. I used "sneaky" as my variable, but you can really use whatever you want (as long as you change the commands as appropriate). To set this up, you just need to use the command /scoreboard objectives add sneaky dummy. You only need to do this once.

I had to set up the command blocks in a very specific pattern for them to work, as shown:

I think this has something to do with how command blocks handle firing off "simultaneously". The comparator in this setup is in subtraction mode, creating a "comparator clock" which pulses very quickly.

The command blocks on the left are your scoreboard related commands. The one on the bottom left sets "sneaky" to 0 for all players:

/scoreboard players set @a sneaky 0

The command block on the top left sets "sneaky" to 1 for all players with the stealth boots equipped:

/scoreboard players set @a sneaky 1 {Inventory:[{Slot:100b,tag:{display:{Name:"Stealth Boots"}}}]}

The command blocks on the right are your effect commands. They give players the invisibility effect, or take it away, as appropriate. The one on the bottom clears the invisibility effect from all players without the stealth boots:

/effect @a[score_sneaky=0] 14 0 0

The top one gives the invisibility effect to all players with the stealth boots:

/effect @a[score_sneaky_min=1] 14 30000