What in your opinion are the best museum's etc worth a visit.
No problem - personally I reckon in a couple of days you should take in the River Promenade (Duna Rakpart) and definitely see the Terror Museum on Andrassy ut, the couple of Arts Museums on Heroes Square, or just the square itself, at the end of Andrassy and have a wander round the Castle District on Var Hegy and the old inner city of Pest. Gellert Hegy has the best views from the statue.
If you fancy the baths, I suggest Szechenyi Furdo in the City Park (also next to Heroes Square).
Mainly on a first trip I recommend soaking up the atmosphere, have a good look round and you will find the things to go back and see next time, plus those not so touristy things such as the fantastic railway station built by Effiel (of the Tower fame) at Nyugati Palyudvar.
Try the public transport rather than your own wheels or whatever. You can buy a 5 day ticket 'tourista jegy' which allows you on just about everything. Don't worry about language, but do get a basic phrasebook and learn how to say please and thank you in Hungarian - it does matter and make a difference. For reference and ease of memory - you need to 'be a rat' to get in and 'kill a rat' to get out of places (you will see what I mean from the signs). 'Fele' means towards.
On an evening you could even visit the Klub Vittula
http://www.vittula.hu/ (see caboodle listings) for a laugh - if you do tell Tim that 'the other Tim' sent you!
or Valhalla for a slap up meal and shoot pool all evening.
Have a good trip!
