Oh Ma Achin' Knees!

In which case you need to proceed carefully! However, don't be bummed out about it, there's plenty you can do - keep a really positive attitude.

What I understand about cycling and knee injuries is that cycling puts your joints through a very controlled range of movement. You can only do yourself damage if one of two things happens: you lack stability in the joint (and this will be an issue with menisci injuries); you're loading your knee in an abnormal manner. Fortunately, both of these issues can be addressed: stability can be gained by strength training (not just the big muscles, but also all the supporting muscles and your core group); abnormal loading by proper positioning on the bike and the pedals (which will involve finding a pair of pedals that gives you the movement and position you need to make your body work), and, of course, gearing down so you reduce the amount of force going through the knee.

Getting yourself into a position when you can ride regularly may take some time and effort but is definitely achievable if you put your mind to it. (Why not write a blog too about your efforts - my gf found a really informative blog by an active sportsman recovering from an ACL injury and it was both really helpful and inspiring). View it as a challenge not a hinderance!

First off, I would find a good physio who's also a cyclist (and ideally has coached cyclists). They'll be able to make sure you're not doing yourself damage and can ensure you've got enough stability and, if not, give you a training plan to give you that stability.

Go and find a good pilates teacher for extra stability work.

Get fitted, as others have said. Buy new pedals at the same time and work out what might work. (Speedplay & Time are the obvious two candidates for good biomechanics)

Take it easy!

Courant

Thanks for the advice and encouragement, I have been looking at this whole thing as way more of a problem than a challenge. It's hard when you go from riding every day and feeling great to turning into a flabby out of shape couch potato in a matter of three months. It's all getting better fast though.

I'm gonna go drink some beer eat some crisps and watch worlds most amazing videos now! Cheers!