It depends on your wallet size and your preferences.
On the low end...........you have "one for all" remotes
http://www.ofausa.com/
These are button remotes that are fairly programmable and under $50. They allow pretty good programming especially if you get the jp1 cable to link to your pc.
My next choice (and in my opinion a step up) (and I am biased and own 2 of them) is the Mx 500 by home theater master/Universal remote control, inc.
http://universalremote.com/htm/
It has really come down in price recently and runs about $80 now via internet (I paid almost 3X as much for my first one). I recommend actually buying this with one of the "one for all remotes" as well, to help program discrete and advanced codes, and because the internal databases for these are much better (and you can buy a cheap one for all for under $20).
The Mx series has the advantage of having an LCD screen that allows 2 screens of 10 buttons for each device, giving you the advantage of actually being able to remember what you programmed where (a problem I sometimes had using a "one for all" remote as my primary remote). Some dealers actually bundle the Mx500 with a one for all, on on occasion with a one for all AND a jp1 cable. It has a very functional light, so you can see all the buttons in the dark, and with the tactile/buttons once you know where the common ones are....you can often use frequently used features without even looking down.
If you are willing to spend more......there are better MX models (look under the "complete control" section in URC website
http://universalremote.com/complete_control/
The MX 650 and MX 850 offer more programablity and in the case of the 850 PC programming.
There is also a large following for touch screen remotes and advantages and disadvantages of button vs. touchscreen. They range from black and white pronto remotes up to the MX 3000......ranging from a couple hundred to almost $1000. These are very programmable, and allow great customization, but again it is a preference thing.....and depends on your desires.....what you want to do with the remote....and your pocketbook. These allow the most customization.
I personally think you get more bang for your buck...and almost enough remote for most basic situations from the mx 500...but ask around.......and check out remote central......where the only topic is remotes....they have a forum for each make remote....as well as general ones.
http://www.remotecentral.com/cgi-bin/mboard/forums.cgi
And a long answer to a short question.....you should be able to put your native remotes away entirely and just keep the universal remote out. The only time in years that I have brought the others out, is when I want to fine tune the placement of buttons or when I buy a new device.