Hi Irish Gunner,
Johnny's is not that far out really, probably just looks far out but is probably about 10 mins walk from the opera at the most. Flanagan's will be more touristy, whereas Johnny's is the haunt for the ex-pats and true Viennese pub fans...
Had a quick thought about what you could do other than the usual museums and tour around the 'Ringstrasse', had planned to take more time thinking about it, but kind of ran out of time....:
http://en.wikipedia.org/wiki/Naschmarkt Vienna's most famouse food market - and plenty of things to eat while you're there (daily) and cool and unusual flea market (Saturdays). Not just for the tourist but all the Viennese people go there, too.
http://en.wikipedia.org/wiki/Wurstelprater Vienna's famous amusement park (the famous ferris wheel is there) - there's some nice food out there, too (although do not expect fancy!) The ferris wheel is good to get a good view of Vienna, as is the Donauturm
http://www.donauturm.at/en/Default.aspx or you can walk up the tower of St. Stephen's cathedral (millions of steps though!)
Some tours or exhibitions and stuff:
http://www.wienguide.at/epages/index.php?page=detail&idtour=1 Third Man Tour - apparently quite good
http://www.verliebtinwien.at/html/english.html For other unconventional tours
http://www.albertina.at/cms/front_content.php?idcatart=64 nice exhibitions in March
http://www.ostermarkt.co.at/files/info_en.html Easter market in front of the castle
Food
http://www.amerlingbeisl.at/
http://www.figlmueller.at/ (Wollzeile restaurant - the most famous Wiener Schnitzl in town)
For more ideas check out
http://www.lonelyplanet.com/worldguide/austria/vienna/where-to-eat My ex wrote the vienna guide, so I hope he hasn't lost his good taste!
http://www.flex.at/ (the hottest club in town)
http://www.dorotheum.com/en/auctions.html (auction house if you want to look at some unusual things - everything from furniture to jewellery)
Also would rather go to budapest than bratislava, the latter hasn't got that much to offer in my opinion. Having said that, it's a good 10 years since I've been there, but I remember not liking it much...
If you're interested in the second world war, there is a concentration camp about 2.5 hours from Vienna by train. Not for the faint-harted though. If you're interested let me know and I post more info on how to get there.
Anyways, hope you enjoy the trip, let me know if I can help in any other way (like getting to form airport, public transport or stuff like that)