Another simple trick/countermeasure would be to have a room filled with a couple inches of water. I don't care if you're transparent, you're still going to leave
very easily spotted wakes as you splash around.
Now, if the BBEG happened to have some form of
Electrical attack, like
Lightening Bolt, and were to target the water with it....
And this sort of situation is one of the key reasons I love
Craft Wonderous Item as the all-time bestest Item Creation Feat. Can everyone say
Goggles of See Invisiblity? I knew you could! Darn, now I'm going to have to make a note to have my own Wizard create/craft a set or three of these in the campain I'm currently in.
You could also make up something like a
Lamp of Invisibility Purge. If it's not inconsipicuous enough just add the
Purge spell to an
Everburning Torch, it's already a known magical item and would be assumed to have a magic aura. These would be ideal for placement at any Palace/Castle gate or portal to keep those sneaky types from slipping past your sleepy guards. Ok, that's
two notes I have to make to myself, I love PDA's.
If you want pure Core stuff there's the old stand-by of
Dust of Appearance, dirt cheap (as magic goes) and oh so effective, not to mention anyone can use it (especialy the blow-tube version). And it's 100% core as well.
Hatchling Dragon