As far as I know, the way Gmail handles conversations and archiving is unreplicated by any desktop client, and single-handedly the most powerful thing about Gmail. I now have a regular habit of archiving any message that doesn't have an actionable item, decluttering my inbox. If another message should arrive in a thread, I have the entire conversation history right there. A good desktop app could replicate it, but I could see this behavior being difficult to map on top of a standard IMAP server.
In addition, there are a ton of innovative small features (especially in Labs - Don't forget Bob!/Got the wrong Bob? have saved my ass multiple times with new clients) that I just don't see other e-mail clients implementing, and they're constantly rolling out new ones. The fact I can get the exact same functionality on any computer I happen to be on is just icing on the cake.
Ultimately: it feels like desktop clients have largely stagnated, while Gmail has an incredibly effective way of thinking about e-mail.
Have you looked at Outlook 2010. They have a similar conversation view. Outlook also gives you the ability to respond to mail with a phone call (Google must have this capability with Google Voice, but don't see it).
Another feature I like with Outlook 2010 is to see all correspondence from the person I'm currently looking at (email, meeting invites, chats, etc...).
There's also this cool thing called Quick Steps, where you can construct macros in Outlook. This is useful when you need to have specific workflow around email that you can put together in one click (like, when responding to legal, I need to send the reply, delete the original email, send another email to my manager, and send a note to OneNote).
And of course Outlook has a webclient, so I can access it from anywhere too. While Outlook is heavyweight, feature-wise, its pretty complete, and offers some other things that are hard to beat.
In addition, there are a ton of innovative small features (especially in Labs - Don't forget Bob!/Got the wrong Bob? have saved my ass multiple times with new clients) that I just don't see other e-mail clients implementing, and they're constantly rolling out new ones. The fact I can get the exact same functionality on any computer I happen to be on is just icing on the cake.
Ultimately: it feels like desktop clients have largely stagnated, while Gmail has an incredibly effective way of thinking about e-mail.