Planning a potential trip to Penang and Langkawi. Ideally will fly in and out of KUL and then book local airlines (Air Asia or MH). Probably KUL-PEN, then do Penang-Langkawi ferry then LGK-KUL for the return flight home with around 4 hours in between.
Any advice for where to stay, and how long would be much appreciated.

Also, there is Batik Air aka Malindo Air - full service carrier with low fares. Between PEN and LGK Firefly is operating ATR72 as well - no need for a ferry!

Also, if you're planning to stay in the city of Kuala Lumpur before and/or after your stay in Penang and Langkawi you might prefer to fly Firefly or Malindo out of Sultan Abdul Aziz Shah airport. This is the old Kuala Lumpur airport located much closer to the city center which makes it very convenient for these flights. Kuala Lumpur International airport is located quite far outside the city.

As said before, there are flights between Langkawi and Penang. Mostly these two destinations are served in one triangle flight from Kuala Lumpur.

If you decide to make a self-transfer in Kuala Lumpur International always check what terminal your airline will be using. Some terminals are quite far apart.

Had a trip down to KUL about 16 months ago. Amazing, vibrant, busy and also very friendly city. Not sure if you have lodging set up yet for KL. If you find yourself with a night or two in KL look at the Aloft Kuala Lumpur Sentral (SPG property, same as Westin, Sheraton, etc). This hotel is great as it is located directly across the street from the KL Sentral Transit/Train station. The hotel is amazing! The rates I found were not terribly bad at roughly $100 US/night. The upside is the location, newer property, amazing roof-top pool, easy access to all KL rail (including monorail). The hotel and the train station are actually linked by an enclosed sky bridge. There is even a huge mall linked to both properties if you have time. You can take the very convenient and affordable train from KLIA to the KL Sentral Station if you choose, avoiding cabs and literally walk across the sky bridge to the Aloft Hotel...it works the same way departing. Some airlines even allow you to check your bags at the KL Sentral Train Station.
As PatrickZ80 mentioned there are 2 airports in KL. Sultan Abdul Aziz Shah is only served by smaller regional carriers utilizing mostly ATR's (Malindo & Firefly). Upside as mentioned about Sultan Abdul Aziz Shah is the close proximity to the city...however I'm pretty sure there is not a "direct" rail link if you were looking to take the train. A couple thoughts about Firefly & Malindo; Firefly is a subsidiary of Malaysia Airlines and operate the ATR 72. While I have not flown them...from my indirect knowledge they seem like they would be fun to fly. They pride themselves on providing some sort of "meal" on every flight...even if it is a juice and pound cake...better than here in the US. I have flown Malindo...only on the B737 though, not on the ATR, so I'm unsure what their level of service is on the shorter routes. I flew them from Bangkok Don Mueang International to KLIA. I opted to spend a tad bit more for a business class seat and must say it was well worth it. Honestly, the fare was quite amazingly low for business class, my seat was generously large with a nice in-seat IFE system and I was served a rather large lunch, which came served on china with as many drinks as I could tolerate.
Hopefully answered some questions for you!

Hey guys,
I once flew Phuket-Penang and return Business Class on Malaysian Airlines, 737-400 one way and 737-500 the other.
The service was astonishingly good. Front row window seat both times and fantastic food.
I MUCH preferred Penang to Phuket... and Malaysia generally to Thailand. I haven't been back to Thailand but I have visited Malaysia a few times since. I can strongly recommend Malacca (or however it is spelt nowadays), even as a (long) day trip from Singapore.
Cheers,
Bunumuring

Thanks for all the replies everyone.
I had actually dismissed staying in Sentral because I had read that it wasn't so "central", but the very convenient proximity to KUL via the Ekspres and the adjacent monorail station means it is better positioned as a starting point to get to KUL. A friend recently stayed there (the Hilton) and found the location convenient and the area vibrant.