What's wrong with any conventional-issue tracker like JIRA, Mantis, Bugzilla etc?
Nothing at all I just want to get a feel for what people are using!
Any pros/cons to them if you have any experience with the above?
I have use Mantis and JIRA extensively. Bugzilla sparingly and don't particularly like how sparse it is.
Mantis is free to host your own instance, fast and lightweight and quite customisable. I like it. Can set up users with permissions. You could have external customers that can only see their own projects etc but that's pretty standard in any decent issue tracker.
JIRA is paid although only $10/month if you are quite small (be aware the next level up gets a lot more expensive, by which stage you might be somewhat locked in). Almost too customisable but you can set any workflow you like so given some time you could make it really well setup. Mantis can do this somewhat too with some customisation
My advice would be just to have a plan/process to log and track issues. How are you going to handle releases, long term issues, what stage is an issue closed or resolved etc.
Make sure you set up custom fields in a way that works for your process. Don't create more than is really necessary or they don't get used.
Really it all comes back to your process.
Aside from that pretty much any issue tracker is going to be better than a spreadsheet or text file that is committed to a repo.