I haven't heard a sub that doesn't sound like a sub yet. 
There's no denying that a sub can take a lot of effort to properly integrate into a high-end stereo system, but once done you would never be without it (except perhaps in a small room).
The intention of a sub is to extend the lower reach of the system without adversely impacting the balance and transparency of the main speakers.
However, to achieve this you need
ALL of the following:
1. high quality sub with excellent damping (HT subs need not apply)
2. measurement equipment & software (and a lot of time) to position the sub optimally and dial it in to the main speakers and room
3. address any significant room mode issues
4. ideally the rolloff slopes of the mains and sub will match for symmetrical crossover (often it is necessary to plug the ports of the mains, sealed mains will usually better integrate with sealed or ported subs than ported mains even though it means raising the xo of the sub).
5. the mains must extend down far enough that the xo point to the sub is low enough that the sub cannot be located by ear and instruments are not dragged toward the sub location.
6. the sub xo should be low enough and steep enough that the sub is 20db or more down by 200hz.
Smaller rooms will introduce room gain at higher frequencies (than larger rooms) and may make sub integration difficult without EQ, indeed a sub may not even be necessary or desirable in these instances.
Room effects often mean that the optimal sub position is not at the same position as that of the mains. This can mean that a separate sub will provide greater flexibility and a more balanced FR than one that is integrated into the main speakers.
Proper integration of a sub should make the music more open and effortless, more extended and impactful at low frequencies, and more balanced with greater dynamic range. Most of the time, you should be unaware that the sub is even there.
Most people don't have the measurement equipment and software to do this properly and have to resort to dialling in the sub by ear. This is extremely difficult to do well (I don't think I could do it) and can be very time consuming and frustrating. Most people feel they should 'hear' the sub and end up with a xo level or gain level that is too high and doesn't blend properly. Most people are also using ported mains and do not try stuffing the ports for better integration. Many subs have fixed xo points (eg. 80hz) or cannot be set low enough to prevent too much overlap, and are underdamped (easier and cheaper) sometimes deliberately for greater HT 'impact' (though inappropriate for high-end HT setups anyway... car doors should NOT sound like explosions!). Many people do not consider the rollof slopes and damping of the mains and sub when adding a sub. All these factors collude to ensure that only a small precentage of people actually optimise the integration of a sub for 2-channel systems.
If a sub is muddying up the upper bass or mids, or causing some lack of coherency or transparency, then the above criteria have not been adequately met.
Of course, all this is IMHO and IME. Many of you already know all this and more, but for those of you who don't I hope that it is of some use and you realise not to take comments like the one above to mean that subs cannot be beneficial in 2-channel systems. Cheers!
