Melodyne & Audiosnap are pretty essential to my workflow, however they are more often than not incredibly laggy on my system and I'm not quite sure why. It seems to process clips at a decent enough speed, but when it comes to actually editing, the response time of mouse clicks & drags will often be a second or so behind which makes editing incredibly difficult. Even the now time marker will stutter & jump if I hover over an clip with Audio transients enabled. Maybe the issue is actually caused by something completely different, but this what I've noticed the most as I've been doing a lot of comping & editing lately. Latency is set at 12ms & 1024 samples. The projects aren't too resource heavy either...8-10 instrument tracks with ProChannel modules.
 
I have a fairly high powered system (Quad Core Athlon with 12GB ram & SSD drives) along with a 1gb video card. My audio card is an EMU 1212m but I also occasionally use a VS-100 in a USB 3 port. So I'm thinking my system just needs a tuning but I'm not exactly sure where to start. Using X3e FWIW.

Another annoyance I've found is that the cursors for envelopes don't show up properly. When hovering over different parts of the envelope, the cursor will flicker for a second but remain as a generic pointer. I'd say it's video card related, but that wouldn't cause the lag I experience in other places. Anyone have suggestions of things I should look at/try?

Still having issues with this if anyone has input. I've updated all my drivers  to the latest, and tried some general tweaks/tips.
 
Here's a video of the Melodyne issue I'm having right now. If I barely drag/move the cursor, the note blob shoots almost off the screen. I've tried clips of various size, short & long.
 
http://youtu.be/whsNSxeBGDY?hd=1
 

I should also add that I've opened clips up in Melodyne Editor standalone without any trouble, so the problem seems to be in the SONAR somewhere, whether in the .ini/settings or somewhere else...any ideas?

I've seen laggy behaviour when I've had multiple Melodyne tabs open. Is it that perhaps?

It's hard to say because each system is different. 
I'm not familiar with your sound card, I took a quick look and see it's no longer available and that it's made by Creative. That's enough for me to question if it's drivers are up to the task. 
Example..I used to use a Tascam us1641 and would have those same problems you are having. Since I switched to a Focusrite the issues have gone away. It's the drivers. 
 
Other than that make sure you optimize your computer and check with Latency Mon for background issues.