I have been working in Support / Technical Services for many years now and have seen my fair share of CRM / Helpdesk Applications. These vary from the big guys Seibel, Remedy, HEAT all the way to free PHP scripts with a messy web front end.
One I’ve seen recently is Kayako’s SupportSuite. This is a web (PHP) based front end with a mySQL back end. It is incredibly feature rich, covering just about ALL of the needs of a typical ISV type company. It is certainly not one of those boxy, bordered table basic HTML front ends either, it actually looks really cool. 
Some of the features I’ve explored so far include :-
- Multiple SLA’s depending on customer
- Good choice of integrated login scenrios (LDAP, vBulletin and many others)
- Intelligent email parser
- Customizable workflow
- Excellent customer facing front end so they can view / edit their cases
- Good knowledgebase, with internal and external articles and an option to auto suggest relevant articles
- Integrates with Outlook
- RSS’able absolutely everywhere (tickets, knowledgebase, news etc)
- Add ons for instant desktop alerts and for live support (web IM)
The only things that I can see that lets this gem down are :-
- A lack of decent support, so far I’ve had a couple of poor answers to one good one and the response times can be lengthy.
- A lack of decent documentation, their docs are so far behind the code it’s untrue – that said it is very intuitive
These guys really could clean up with this, I can see how I could have easily used this (and improved productivity) at all the companies I’ve worked for. It’s a real shame about the support and docs, it just makes it that much harder to implement, extend and operate. Does a busy support department really have the luxury to wait a day or two for support on their issues.
Although you get 98% of the source code when you purchase (a snip at $500 USD) the ‘owned’ version (I guess the 2% is their licensing code), how cool would it be to take a ‘Integration / Customization guide’, work through it and end up with a neat product streamlined to your business processes and systems – not going to happen right now with no docs, instead you’d have to pick through the PHP code by hand
I love this application, come on guys, you’ve got most of the NEEDED features in there already, get the docs and support sorted out, you could clean up !!