We visited the Outer Hebrides in April last year. We were blessed with beautiful weather. We travelled north to south and if we do it again would do the reverse and travel south to north as I think the islands get better as you go north. We messed up our timing a bit and spent too little time in the north and too much in the south.
The Calmac Island Rover ferry tickets were extremely good value and very flexible
http://www.calmac.co.uk/tickets/island-rover.htm
There aren't many proper campsites on the Islands - the few that are there are all pretty good though! And there are lots of places to wild camp.
The places we would definitely go back to are: (from south to north...)
The community hall at Vatersay. Almost wild camping - there was an honesty box (£5 per night?) and a single loo. Stunning walks and fascinating history...
On south west South Uist there is a picnic spot at the end of the road past Gearraidh ma Monadh we wild camped here. Very quiet.
Again on South Uist we didn't stay here but we met a couple that managed to get their rather large camper van onto one of the best wild camping spots I've ever seen. Take the single track road to Loch Sgioport and they were parked right down at the end of the steep-ish track - with the back of their van hanging out over the sea! Worth a look even if you don't stop there.
Shelby Campsite on Benbecula is handy. It is just north of the causeway from South Uist to Benbecula. The beaches here were a bit of a mess though with bottles and rubbish.
On North Uist we stayed at Moorcroft - which was a lovely site
http://www.ukcampsite.co.uk/sites/details.asp?revid=8778
The community road which runs across the middle of the island is worth a little drive - we saw a number of Eagles at the top which were huge and beautiful.
On Harris, Horgabost had a basic site with stunning walks and views. There is a stunning semi wild site at Cnip where you pay the lovely lady in the village £5 a night!
On Lewis, we stayed just outside Stornoway and used this site as a base whilst travelling around
http://www.laxdaleholidaypark.com/
There aren't many shops so we stayed pretty well self sufficient.
Enjoy!