I have a similar problem - I'm a University lecturer and outside of teaching duties I have to create my own work (e.g. grant applications, designing experiments) and sometimes I just cannot. Be. Bothered!
I've found that GTD is very good for organising tasks, but not so much for keeping you ON task. I do what you mentioned in your OP - set a timer (usually half an hour), pick a project that I need to work on and do that for the time. If I have to stop for some reason (e.g. the phone rings) I pause the timer. Then after that half hour, I get ten minutes to do whatever I want. Any website surfing or messing about is allowed.
This REALLY helps, because if you find yourself drifting you just look at your timer and say "no, I'll do that in x minutes". It's much more specific than saying "I'll do it when I've finished", and so the impulse is easier to resist.
This sounds very like the pomodoro technique which I read about here last week, and I've actually adjusted to do 25 minutes work, 5 minutes rest. In the 5 minutes, I do NOTHING. Just sit and let my brain chill out! Unlike the technique specification though, if I'm still going after 25 minutes I carry on until I find myself drifting. It's 25 minutes "compulsory" work, and then after that you can stop whenever you like, and have your "rest".
It's surprising how much easier it is to get down on a project that you've been resisting if you say "this is just for 25 minutes" rather than "ugh I need to do this now and I don't know when I'll finish"
Include a longer lunch break or rest at some point too - you need to eat and fuel up otherwise you won't think properly!