In order to eliminate clicks in words in Pro Tools, and I use either the Pencil Tool or cut out a cycle of the waveform.
What would software tool would you recommend?
I'm all about iZotope RX. It's such a lifesaver for me. I do everything from lowering the noise floor on recordings, removing clicks and clipping, to removing a cough from a live music performance (I actually got that one to work perfectly!! I'll have to see if I can find the original and final to let you guys A/B the two).
If it's something really tiny and don't want to spend time in RX (it can be very time consuming for more complex fixes), I'll go with the old pencil tool trick.
When i really want to get that click out manually, i cut and paste. Each phoneme tends to have a repeating wave cycle, so i zoom in til i see the wave and grab one of the cycles before or after, and paste it over. A small crossfade may be necessary. The pencil tool only lowers the amplitude of the click, it doesn't completely get rid of it.
It's only really good for glitchy clicks, as clicks recorded in the space will have a reverb tail.
For quick "one click" click removal, the old Sonnox Declicker is outstanding - haven't used their new one, though...
For "musical clicks" I like to use iZotope's Spectral Repair - amazing flexibility in certain situations.
Can't beat good old room tone fill for a lot of clicks... it all depends on the time you have and the "type" of click you're dealing with.
If editing in Protools then I'll mainly cut out cycles over using the pencil tool, but I'll use that if needs be. If I'm working to picture, then I just take a little more time to check that the sync's not been compromised. After all - picture work is mainly FPS and cutting out a cycle is tiny samples.
If I have a really clicky piece then I'll use Audition as I've recently been introduced to the spectral editing tool which is, on one hand, cheating (ie not using your ears) and on the other as fast as lightning.
I'll have a proper look into XClick though :)