I like the HTC keyboard, but I also like the stock Gingerbread keyboard too. In fact, in my Samsung Galaxy S2, i got the standard Gingerbread keyboard installed as default.
Both HTC Sense and vanilla Android has both their pluses and minuses.
HTC Mail client - Do you know you can set up GMail on this client and actually get pinch and zoom viewing too? (Sort of like the iPhone mail client). The standard GMail client doesn't pinch and zoom.
vs.
Standard email client - What I dislike about the HTC Mail client is that although it has support for multiple Exchange accounts, I can't set up m.hotmail (the push version of Hotmail) on it. It prefers to use the default, wizard setup Hotmail. On the standard Android email account, there is an alternative way to set up Hotmail that will let you get push notifications instead of POP3. The Samsung stock email account is closely patterned after the stock Android client and has this as well.
Gallery
HTC Gallery is fast, has direct Flickr upload. If you set up Flickr account sync with Friendstream, it will sync Flickr photos too. However it lacks Picasa support.
Standard Gallery (also known as the Nexus Gallery). --- also seen on the Samsung phones as Samsung wisely chose not to modify this app. No direct Flickr support but it has native Picasa cloud integration. That will help you if you are a Google+ user.
If you are using Google+, I noticed problems with the Instant Upload feature of the Android Google+ app. HTC Sense actually stores pictures on a separate partition than than what the stock Nexus Gallery app does. You can actually download a copy of the Gallery app from the Android Market and install it on your HTC phone. You will notice it won't show the pictures you took because the way the pictures are stored.
Facebook
Friendstream is a nice app to see your Facebook and Twitter feeds with. For some reason I can't post on Facebook recently and that must have been the result of some API change in Facebook.
The one thing I don't particularly like about HTC is that they replace the original Facebook sync, which is provided for you when you install the original Facebook app for Android. What HTC replaced it was Facebook Sync for HTC Sense. You can't set up the original sync and the Facebook app itself now has to use this sync. However, push notifications on the original Facebook app or Facebook Messenger doesn't go through this anyway.
Of course, the reason why HTC disables Facebook sync and insists on using theirs is to prevent duplication in syncs.
On the Nexus S, due to a tiff with Facebook, from Android 2.3.3 and 2.3.4, you will see the original Facebook sync disabled. This is for contacts, which means your Facebook contacts won't be syncing into your phone directory. However, it doesn't stop push notifications. Gingerbread actually has better push notifications for Facebook especially if you installed Facebook Messenger --- you can see the portrait of the contact in the notification on the curtain itself.
I'm using a Galaxy S2 right now. The Samsung, unlike HTC, allows for the original Facebook sync, even though it has a separate Facebook sync of its own (Facebook Sync for Social Hub). But again, this can result in duplicate syncs if you fail to turn off the Sync Contacts in the Social Hub account.
While Samsung does allow Facebook to sync contacts into the phone book (every Android does except the Nexus S), Samsung doesn't have the automatic linking between duplicate entries on the contacts book unlike HTC.