Having just invested in an Ipod, are there any podcasts I should be looking out for to listen to whilst on the train etc?

That would depend on what interests you. Just search Itunes or use any search engine on your area of interest and something should come up. What ever you find there should be a huge back catalogue for you to wade through.

I listen to science, scepticism and atheism podcasts of which "The Skeptics Guide To The Universe" is the most popular. The best home grown podacst of the genre is probably "Skeptics with a K" by the Merseyside Skeptics.

TEDTalks would be good podcasts. Think they do video ones, so possibly audio too.

Also depends what you're into. I used to listen to a few which were basically radio shows without the music. All the highlights.

Adam & Joe, Jon Richardson from 6Music were my main ones. Oh, and Danny Wallace when he was on XFM a long time ago

I listen to the Freakonomics podcast and have done for ages - it's consistently excellent; I also like More or Less off of Radio 4.

As a massive movie fan, I was deeply disappointed with the Empire podcast; it's like listening to 3 slightly drunk people who are convinced of their own hilariousness talking in a pub - fun for them, but grating for everyone else.

I hear that Greatest Events in Sporting History is pretty good, now that I have the shameless plug out of the way I will give you some advice.
The BBC are pretty good resource for podcasts since they put out quite a lot of their shows out in podcast form, meaning there is a large selection of very well produced shows, just a case of finding a topic.
It really is a case of searching for your own interests, reading the reviews and taking a chance, there are a whole load of podcasts that I have only ever listened to one show of.
If you list some of your interests here, maybe people point you in the right direction

As people have said it depends on your interests, I get the Kermode film review and Martin Lewis podcasts from 5Live

Just working my way through the desert island discs archive.

Thanks for the suggestion - such a good call, I'm sitting here painting tonight with one desk lamp on listening to Dawn French on DiD, really good stuff.