There are three remote (families) I consider tops.

1) Pronto (there are a lot of remotes that fit in this group and they range in price from a bit over 200 to over 1000 you can read the review of the TSU-2000, TSU-6000 and the Yamaha RAV-2000. The ones I like the most are the Pronto, ProntoPro, RC5200, RC9200

2) the HTM MX-500 (the 700 also looks interesting, but since it is not out yet, I cannot judge it)

3) The Harmony remote from easyzapper

Daniel has reviewed all of these three types, read his reviews, they are very informative. They all have their supporters, and since they are all very different a lot is based mostly on personal likes and dislikes.