I usually stand by Wario Land, but my preference comes from my love for 2D platformers.
So I'd say both are equally great.
The Wario Land is just well made overall. The graphics are appealing and fun to watch, the soundtrack is gosh darned perfect, and the level design is genius. Wario controls really nice in those games, with Wario Land 4 being the best. Sadly, in Wario Land Milk Shake, the controls feel stiff... Other than that, it's a really great series and I'm still shocked today as to why there's people who haven't tried it yet. Go grab a copy of Virtual Boy Wario Land, Wario Land II, 3 or 4 and tell me I'm wrong, you'll surely be hooked!
As for WarioWare, well, it was kind of a surprise, really... At first, I just hated it, that blind hate you get when you see your favorite character with a weird look and a bunch of dumb looking characters in one of the pages of your weekly gaming magazine, announcing the next "Wario" game... So I was like "What DA HECK DID THEY DO TO MY BOI WARIO?!"
Anyway, never judge a book by its cover, as once I bought WarioWare Touched (finally), I found myself hooked for DAYS! And everyone around me wanted to play it too!
The games are fun, even the simplistic design and dumb look of the game play a part in it. The soundtrack is perfect, really good music and wacky tunes, jingles and sound effects, perfect to set up the mood, as the game takes you through hundreds of 5 second long minigames in sequence, called microgames. There's not much to say about the controls, they're generally perfect (except for the forgotten WarioWare Snapped, which is definitely ok to forget, btw).
Although I love both franchises for how unique they are, both of them became bland when both titles came to the Wii. Yes, probably my least favorite console had both Wario Land and WarioWare, and let me tell you, I wasn't happy... Wario Land Shake Me is really good, as I stated earlier, but those controls feel sooooooo stiff compared to Wario Land 4, that I just can't enjoy it as much... I had high hopes when I saw the new handdrawn graphics, and the soundtrack in the trailers, those are the best that the game offers, sadly, I get bored of it quickly...
As for WarioWare Smooth Moves... well, you have to move a lot in that game. That's not a problem, it's actually a fun gimmick, but since the Wii controller wasn't accurate at all, before the Wii Motion Plus, the controls fail for no reason. Plus, like I said, the motion gimmick is not bad, but it gets old quickly, comparing to the touch controls, which work really well and still stand today. If you ask me, other than that, there's nothing else wrong with the game, it's actually great, but it will definitely not be the best, for sure, as all games post WarioWare Touched feel slow and softened, losing the "crazy and wonky" charm of those past titles. Remember what other franchise suffered from that? Mario Kart. Yes, compare how crazy Mario Kart Double Dash was with how slow and soft Mario Kart DS turn out.
Oh well, overall, both series are near perfect, and I'm sure there's still room for one more title for each. Please, Nintendo, make it happen, the fans are crying. (It was Wario Land that got me into playing Nintendo. I knew I would get Wario games if I played Nintendo consoles, so I stuck with it. Also, I'm not sad about not having a N64, for that exact reason: No Wario games).