It's all in the drums - where the "accents" (usually snare hits) fall.
Here's Wikipedia's version of it...
3/4 is a simple signature that represents three quarter notes. It has a basic feel of (Bold denotes a stressed beat):
one two three (as in a waltz)
Each quarter note might comprise two eighth-notes (quavers) giving a total of six such notes, but it still retains that three-in-a-bar feel:
one and two and three and
6/8: Theoretically, this can be thought of as the same as the six-quaver form of 3/4 above with the only difference being that the eighth note is selected as the one-beat unit. But whereas the six quavers in 3/4 had been in three groups of two, 6/8 is practically understood to mean that they are in two groups of three, with a two-in-a-bar feel (Bold denotes a stressed beat):
one and a, two and a
or
one two three, four five six
Essentially, it's the same amount of notes but different accents of them. For Windowpane, the beat is as follows:
o = kick
O = snare
x = cymbal
6/8: oxoOxo
3/4: oxoxOx
Rinse and repeat, at least for the intro riff and its reprises. I believe the rest of the song is in 4/4.
For ease of simplicity, some tabs and sheet music will not differentiate between these bars because they're primarily focused on melody instruments and not percussion. The difference between 6/8 and 3/4 is not mathematical, but rather a "feel." 6/8 is a "triplet" groove, where 3/4, much like 4/4, is a "straight" groove.
Two excellent non-Opeth songs that feature the same guitar riffs but where the drummer changes the beat underneath to make it sound like an entirely new riff (due to the accents) are the solo section in Dream Theater's "Panic Attack" and the verses of Symphony X's "Prometheus (I Am Alive)." It might give you a clearer understanding of this.
Hope it helps!