STEVE HARRIS  Together shouldn't use any CPU when you're not using it, unless it's doing something (e.g. generating thumbnails), so I would need to check what was going on.

If you need support, visit my site: http://reinventedsoftware.com/support/

Thanks.  
(Version 2.2.13)

STEVE HARRIS  Together uses an Mac OS X technology called Latent Semantic Mapping for its auto-tagging feature, which works out the most likely tags based on the tags you already have used for similar content.

If you look at the textual content of the xkcd home page (e.g. the very, very small print down the bottom), it actually mentions things like algorithms and mathematics, so that probably explains this case.

The tagging is smart though, so if you were to change the tags on those, it will start to learn that web pages that mention both algorithms and humor are not the same as the others in your library.  
(Version 2.2.5)

STEVE HARRIS  I didn't notice this until posting the 2.2.4 release but for the record, version 2.2.3 fixed the problem with slow imports in 2.2.2 and, thankfully, I haven't heard of any MobileMe syncing issues since Mac OS X 10.5.6 was released.  
(Version 2.2.4)

STEVE HARRIS  Version 2.2.1 should have addressed the crashing, which was down to the new auto-tagging feature. I can't identify any crash reports using your MacUpdate name, but I'd be interested to hear from you so I could look into your problems.

On the option being greyed out to save a web page as a PDF, I don't know which option you mean, and as no one else has reported a problem with this, I can't really comment. Get in touch if you need help. Thanks.  
(Version 2.2.1)

STEVE HARRIS  Together allows you to link to files anywhere on your system without needing to move them.  
(Version 2.1.3)

STEVE HARRIS  The previous commenter got their wires crossed about this. Together does use a different format for notes, but all KIT notes will be imported converted into Together on first run, or on demand.

This is made clear in the first line of the KIT import panel shown when Together is launched, which probably explains why nobody had emailed me about this - which is always the best thing to do. I am not informed when new comments are posted on download sites.  
(Version 2.0.1)

STEVE HARRIS  The reason is that you don't need to open KIT notes in Together by importing them individually from KIT as you seem to be doing because Together will import and convert them for you.

On first run, Together will offer to import your KIT library (and you can import KIT libraries at any time with File > Import KIT Library) converting notes, preserving tags, groups, ratings, labels, etc.   
(Version 2.0.1)