2000's Multi-week #1 Single Sales (that didn't peak at #1 on the Hot 100)2000
Jessica Simpson - I Wanna Love You Forever (4 weeks in 1999, 2 weeks in 2000) #3
Toni Braxton - He Wasn't Man Enough (4 weeks) #2
Marc Anthony - You Sang to Me (3 weeks) #2
Mya - Case of the Ex (3 weeks) #2
2001
Dream - He Loves U Not (1 week in 2000, 3 weeks in 2001, total week tally from both Hot Digital Tracks and Hot Digital Songs) #2
112 - It's Over Now (2 weeks) #6
Eden's Crush - Get Over Yourself (2 weeks) #8
City High - What Would You Do (2 weeks) #8
Lil' Romeo - My Baby (6 weeks) #3
Mariah Carey - Loverboy (4 weeks) #2
Janet Jackson - Someone to Call My Lover (3 weeks), #3
Jagged Edge w/ Nelly - Where the Party At (3 weeks) #3
Whitney Houston - Star-Spangled Banner (6 weeks) #6
Lee Greenwood - God Bless the USA (3 weeks), #16
2002
B2K - Uh Huh (10 weeks) #37
Mr. Cheeks - Lights, Camera, Action! (2 weeks) #14
N'Sync feat. Nelly - Girlfriend (14 weeks) #5
Elvis Presley - A Little Less Conversation (3 weeks) #69
Wyclef Jean feat. Claudette Ortiz - Two Wrongs (3 weeks) did not chart
Dixie Chicks - Long Time Gone (5 weeks) #7
Nivea feat. Brian and Brandon Casey - Don't Mess with My Man (2 weeks) did not chart
Madonna - Die Another Day (8 weeks in 2002, 3 weeks in 2003) #8
2003
Kid Rock feat. Allison Moore - Picture (12 weeks) #4
Mariah Carey - Through the Rain (2 weeks) #81
American Idol Finalists - God Bless the USA (8 weeks)
Hilary Duff - So Yesterday (2 weeks) #42
Elvis Presley - Rubberneckin' (2 weeks) #94
Mercyme - I Can Only Imagine (10 weeks) #71
2004
Eamon - f**k It (I Don't Want You Back) (9 weeks) #16
Beyonce - Me, Myself, And I (3 weeks) #4
Clay Aiken - Solitaire/The Way (9 weeks) #4
Jessica Simpson - Take My Breath Away (2 weeks) #20
Nitty - Nasty Girl (4 weeks) did not chart
Brooke Hogan - Everything to Me (2 weeks) #97
Destiny's Child - Lose My Breath (6 weeks in 2004, 8 weeks in 2005) #3
2005
Destiny's Child - Soldier (5 weeks) #3
Natalie - Goin' Crazy (5 weeks) #13
American Idol Finalists Season 4 - When You Tell Me You Love Me (6 weeks)
Pussycat Dolls (feat. Busta Rhymes) - Don't Cha (10 weeks) #2
Madonna - Hung Up (4 weeks) #7
2006
Nine Inch Nails - Everyday Is Exactly the Same (5 weeks) #56
Beyonce - Deja Vu (3 weeks) #4
Janet (Jackson) & Nelly - Call on Me (6 weeks) #25
Jebbs - Chain Hang Low (2 weeks) #7
Jeff Foxworthy/Bill Engwall - Redneck 12 Days of Christmas Here's Your Sign (2 weeks) did not chart
2007
Rich Boy feat. Palow Da Don - Throw Some D's (3 weeks) #6
The Fratellis - Flathead (3 weeks) #73
Beyonce - Listen (6 weeks) #61
Artic Monkeys - Brianstorm (2 weeks) did not chart
Beyonce & Shakira - Beautiful Liar (2 weeks) #3
Mandisa - The Only World (5 weeks) did not chart
High School Musical Cast - What Time It Is (20 weeks in 2007, 2 weeks in 2008) #6
2008
The White Stripes - Conquest (2 weeks) did not chart
Madonna feat. Justin Timberlake - 4 minutes (2 weeks) #3
Camp Rock Cast - We Rock (5 weeks) #33
*Could not find data on Feb, Apr, July 12-onward
2000's Multi-week #1 Digital Songs (that didn't reach #1 on the Hot 100)*taken from the Hot Digital Tracks chart, which did not count toward total Hot 100 chart points
2003
John Mayer - Bigger Than My Body (2 weeks) #33
2004
Maroon 5 - This Love (4 weeks) #5
D12 - My Band (3 weeks) #6
Hoobastank - The Reason (10 weeks) #2
Maroon 5 - She Will Be Loved (5 weeks) #5
U2 - Vertigo (4 weeks) #31
Bowling For Soup - 1985 (4 weeks) #23
Jay-Z/Linkin Park - Numb/Encore (2 weeks) #20
2005
Green Day - Boulevard of Broken Dreams (1 week in 2004, 6 weeks in 2005) #2
See
this post for the rest of the decade.